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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs1469771626

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:27301828 (GRCh38.p14) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000007 (1/140246, GnomAD)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NEK10 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 140246 T=0.999993 G=0.000007
gnomAD - Genomes European Sub 75952 T=0.99999 G=0.00001
gnomAD - Genomes African Sub 42028 T=1.00000 G=0.00000
gnomAD - Genomes American Sub 13654 T=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 T=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 T=1.0000 G=0.0000
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p14 chr 3 NC_000003.12:g.27301828T>G
GRCh37.p13 chr 3 NC_000003.11:g.27343319T>G
Gene: NEK10, NIMA related kinase 10 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NEK10 transcript variant 1 NM_001031741.5:c. N/A Genic Upstream Transcript Variant
NEK10 transcript variant 4 NM_001304384.3:c. N/A Genic Upstream Transcript Variant
NEK10 transcript variant 3 NM_199347.4:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform 3 NP_955379.2:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant 2 NM_152534.6:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform 2 NP_689747.3:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant 8 NM_001394966.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform 8 NP_001381895.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant 5 NM_001394963.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform 5 NP_001381892.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant 10 NM_001394968.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform 10 NP_001381897.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant 12 NM_001394970.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform 2 NP_001381899.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant 6 NM_001394964.1:c.949A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform 6 NP_001381893.1:p.Asn317His N (Asn) > H (His) Missense Variant
NEK10 transcript variant 9 NM_001394967.1:c.949A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform 9 NP_001381896.1:p.Asn317His N (Asn) > H (His) Missense Variant
NEK10 transcript variant 13 NM_001394971.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform 7 NP_001381900.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant 7 NM_001394965.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform 7 NP_001381894.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant 11 NM_001394969.1:c.949A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform 11 NP_001381898.1:p.Asn317His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X1 XM_017005763.2:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X1 XP_016861252.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X2 XM_017005765.2:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X1 XP_016861254.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X3 XM_017005762.3:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X1 XP_016861251.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X5 XM_017005764.2:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X1 XP_016861253.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X6 XM_006712998.3:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X2 XP_006713061.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X7 XM_006712999.4:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X3 XP_006713062.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X8 XM_017005768.2:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X4 XP_016861257.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X9 XM_047447505.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X5 XP_047303461.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X10 XM_006713001.4:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X5 XP_006713064.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X11 XM_047447506.1:c.949A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X6 XP_047303462.1:p.Asn317His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X12 XM_047447507.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X7 XP_047303463.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X13 XM_047447508.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X8 XP_047303464.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X14 XM_047447509.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X9 XP_047303465.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X15 XM_017005774.3:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X10 XP_016861263.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X16 XM_047447510.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X11 XP_047303466.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X17 XM_011533414.3:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X12 XP_011531716.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X18 XM_047447511.1:c.1036A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X13 XP_047303467.1:p.Asn346His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X19 XM_047447512.1:c.949A>C N [AAT] > H [CAT] Coding Sequence Variant
serine/threonine-protein kinase Nek10 isoform X14 XP_047303468.1:p.Asn317His N (Asn) > H (His) Missense Variant
NEK10 transcript variant X4 XR_001740034.2:n.1272A>C N/A Non Coding Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= G
GRCh38.p14 chr 3 NC_000003.12:g.27301828= NC_000003.12:g.27301828T>G
GRCh37.p13 chr 3 NC_000003.11:g.27343319= NC_000003.11:g.27343319T>G
NEK10 transcript variant 2 NM_152534.6:c.1036= NM_152534.6:c.1036A>C
NEK10 transcript variant 2 NM_152534.5:c.1036= NM_152534.5:c.1036A>C
NEK10 transcript variant 2 NM_152534.4:c.1036= NM_152534.4:c.1036A>C
NEK10 transcript variant 2 NM_152534.3:c.1036= NM_152534.3:c.1036A>C
NEK10 transcript variant X10 XM_006713001.4:c.1036= XM_006713001.4:c.1036A>C
NEK10 transcript variant X16 XM_006713001.3:c.1036= XM_006713001.3:c.1036A>C
NEK10 transcript variant X14 XM_006713001.2:c.1036= XM_006713001.2:c.1036A>C
NEK10 transcript variant X9 XM_006713001.1:c.1036= XM_006713001.1:c.1036A>C
NEK10 transcript variant X7 XM_006712999.4:c.1036= XM_006712999.4:c.1036A>C
NEK10 transcript variant X10 XM_006712999.3:c.1036= XM_006712999.3:c.1036A>C
NEK10 transcript variant X9 XM_006712999.2:c.1036= XM_006712999.2:c.1036A>C
NEK10 transcript variant X7 XM_006712999.1:c.1036= XM_006712999.1:c.1036A>C
NEK10 transcript variant 3 NM_199347.4:c.1036= NM_199347.4:c.1036A>C
NEK10 transcript variant 3 NM_199347.3:c.1036= NM_199347.3:c.1036A>C
NEK10 transcript NM_199347.2:c.1036= NM_199347.2:c.1036A>C
NEK10 transcript variant X15 XM_017005774.3:c.1036= XM_017005774.3:c.1036A>C
NEK10 transcript variant X21 XM_017005774.2:c.1036= XM_017005774.2:c.1036A>C
NEK10 transcript variant X20 XM_017005774.1:c.1036= XM_017005774.1:c.1036A>C
NEK10 transcript variant X3 XM_017005762.3:c.1036= XM_017005762.3:c.1036A>C
NEK10 transcript variant X3 XM_017005762.2:c.1036= XM_017005762.2:c.1036A>C
NEK10 transcript variant X3 XM_017005762.1:c.1036= XM_017005762.1:c.1036A>C
NEK10 transcript variant X6 XM_006712998.3:c.1036= XM_006712998.3:c.1036A>C
NEK10 transcript variant X9 XM_006712998.2:c.1036= XM_006712998.2:c.1036A>C
NEK10 transcript variant X6 XM_006712998.1:c.1036= XM_006712998.1:c.1036A>C
NEK10 transcript variant X17 XM_011533414.3:c.1036= XM_011533414.3:c.1036A>C
NEK10 transcript variant X24 XM_011533414.2:c.1036= XM_011533414.2:c.1036A>C
NEK10 transcript variant X17 XM_011533414.1:c.1036= XM_011533414.1:c.1036A>C
NEK10 transcript variant X1 XM_017005763.2:c.1036= XM_017005763.2:c.1036A>C
NEK10 transcript variant X4 XM_017005763.1:c.1036= XM_017005763.1:c.1036A>C
NEK10 transcript variant X5 XM_017005764.2:c.1036= XM_017005764.2:c.1036A>C
NEK10 transcript variant X5 XM_017005764.1:c.1036= XM_017005764.1:c.1036A>C
NEK10 transcript variant X2 XM_017005765.2:c.1036= XM_017005765.2:c.1036A>C
NEK10 transcript variant X6 XM_017005765.1:c.1036= XM_017005765.1:c.1036A>C
NEK10 transcript variant X8 XM_017005768.2:c.1036= XM_017005768.2:c.1036A>C
NEK10 transcript variant X13 XM_017005768.1:c.1036= XM_017005768.1:c.1036A>C
NEK10 transcript variant X4 XR_001740034.2:n.1272= XR_001740034.2:n.1272A>C
NEK10 transcript variant X1 XR_001740034.1:n.1310= XR_001740034.1:n.1310A>C
NEK10 transcript variant X9 XM_047447505.1:c.1036= XM_047447505.1:c.1036A>C
NEK10 transcript variant 12 NM_001394970.1:c.1036= NM_001394970.1:c.1036A>C
NEK10 transcript variant 5 NM_001394963.1:c.1036= NM_001394963.1:c.1036A>C
NEK10 transcript variant 6 NM_001394964.1:c.949= NM_001394964.1:c.949A>C
NEK10 transcript variant 13 NM_001394971.1:c.1036= NM_001394971.1:c.1036A>C
NEK10 transcript variant 7 NM_001394965.1:c.1036= NM_001394965.1:c.1036A>C
NEK10 transcript variant 8 NM_001394966.1:c.1036= NM_001394966.1:c.1036A>C
NEK10 transcript variant 9 NM_001394967.1:c.949= NM_001394967.1:c.949A>C
NEK10 transcript variant X12 XM_047447507.1:c.1036= XM_047447507.1:c.1036A>C
NEK10 transcript variant X11 XM_047447506.1:c.949= XM_047447506.1:c.949A>C
NEK10 transcript variant 10 NM_001394968.1:c.1036= NM_001394968.1:c.1036A>C
NEK10 transcript variant X13 XM_047447508.1:c.1036= XM_047447508.1:c.1036A>C
NEK10 transcript variant X14 XM_047447509.1:c.1036= XM_047447509.1:c.1036A>C
NEK10 transcript variant 11 NM_001394969.1:c.949= NM_001394969.1:c.949A>C
NEK10 transcript variant X16 XM_047447510.1:c.1036= XM_047447510.1:c.1036A>C
NEK10 transcript variant X18 XM_047447511.1:c.1036= XM_047447511.1:c.1036A>C
NEK10 transcript variant X19 XM_047447512.1:c.949= XM_047447512.1:c.949A>C
serine/threonine-protein kinase Nek10 isoform 2 NP_689747.3:p.Asn346= NP_689747.3:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X5 XP_006713064.1:p.Asn346= XP_006713064.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X3 XP_006713062.1:p.Asn346= XP_006713062.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform 3 NP_955379.2:p.Asn346= NP_955379.2:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X10 XP_016861263.1:p.Asn346= XP_016861263.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X1 XP_016861251.1:p.Asn346= XP_016861251.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X2 XP_006713061.1:p.Asn346= XP_006713061.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X12 XP_011531716.1:p.Asn346= XP_011531716.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X1 XP_016861252.1:p.Asn346= XP_016861252.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X1 XP_016861253.1:p.Asn346= XP_016861253.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X1 XP_016861254.1:p.Asn346= XP_016861254.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X4 XP_016861257.1:p.Asn346= XP_016861257.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X5 XP_047303461.1:p.Asn346= XP_047303461.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform 2 NP_001381899.1:p.Asn346= NP_001381899.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform 5 NP_001381892.1:p.Asn346= NP_001381892.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform 6 NP_001381893.1:p.Asn317= NP_001381893.1:p.Asn317His
serine/threonine-protein kinase Nek10 isoform 7 NP_001381900.1:p.Asn346= NP_001381900.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform 7 NP_001381894.1:p.Asn346= NP_001381894.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform 8 NP_001381895.1:p.Asn346= NP_001381895.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform 9 NP_001381896.1:p.Asn317= NP_001381896.1:p.Asn317His
serine/threonine-protein kinase Nek10 isoform X7 XP_047303463.1:p.Asn346= XP_047303463.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X6 XP_047303462.1:p.Asn317= XP_047303462.1:p.Asn317His
serine/threonine-protein kinase Nek10 isoform 10 NP_001381897.1:p.Asn346= NP_001381897.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X8 XP_047303464.1:p.Asn346= XP_047303464.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X9 XP_047303465.1:p.Asn346= XP_047303465.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform 11 NP_001381898.1:p.Asn317= NP_001381898.1:p.Asn317His
serine/threonine-protein kinase Nek10 isoform X11 XP_047303466.1:p.Asn346= XP_047303466.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X13 XP_047303467.1:p.Asn346= XP_047303467.1:p.Asn346His
serine/threonine-protein kinase Nek10 isoform X14 XP_047303468.1:p.Asn317= XP_047303468.1:p.Asn317His
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

2 SubSNP, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2746962375 Nov 08, 2017 (151)
2 GNOMAD ss2790902202 Nov 08, 2017 (151)
3 gnomAD - Genomes NC_000003.12 - 27301828 Apr 27, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2746962375, ss2790902202 NC_000003.11:27343318:T:G NC_000003.12:27301827:T:G (self)
102523363 NC_000003.12:27301827:T:G NC_000003.12:27301827:T:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1469771626

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post820+afb47a3d