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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.

rs1476170948

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:43540251 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000011 (3/264690, TOPMED)
A=0.000008 (2/251474, GnomAD_exome)
A=0.00000 (0/35430, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
EFCAB6 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 35430 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
European Sub 26586 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
African Sub 2918 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 2804 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 500 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 628 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 4588 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A


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
TopMed Global Study-wide 264690 G=0.999989 A=0.000011
gnomAD - Exomes Global Study-wide 251474 G=0.999992 A=0.000008
gnomAD - Exomes European Sub 135400 G=0.999993 A=0.000007
gnomAD - Exomes Asian Sub 49010 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34592 G=0.99997 A=0.00003
gnomAD - Exomes African Sub 16254 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6138 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 35430 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 26586 G=1.00000 A=0.00000
Allele Frequency Aggregator Other Sub 4588 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2918 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
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 22 NC_000022.11:g.43540251G>A
GRCh37.p13 chr 22 NC_000022.10:g.43936131G>A
EFCAB6 RefSeqGene NG_030019.1:g.277087C>T
Gene: EFCAB6, EF-hand calcium binding domain 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
EFCAB6 transcript variant 1 NM_022785.4:c.3755C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform a NP_073622.2:p.Thr1252Ile T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant 2 NM_198856.3:c.3299C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform b NP_942153.1:p.Thr1100Ile T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X15 XM_011530326.4:c. N/A Genic Downstream Transcript Variant
EFCAB6 transcript variant X17 XM_011530328.4:c. N/A Genic Downstream Transcript Variant
EFCAB6 transcript variant X20 XM_011530330.4:c. N/A Genic Downstream Transcript Variant
EFCAB6 transcript variant X18 XM_047441463.1:c. N/A Genic Downstream Transcript Variant
EFCAB6 transcript variant X21 XM_047441465.1:c. N/A Genic Downstream Transcript Variant
EFCAB6 transcript variant X1 XM_017028910.3:c.3833C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X1 XP_016884399.1:p.Thr1278I…

XP_016884399.1:p.Thr1278Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X2 XM_011530316.2:c.3833C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X1 XP_011528618.1:p.Thr1278I…

XP_011528618.1:p.Thr1278Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X3 XM_011530317.4:c.3755C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X2 XP_011528619.1:p.Thr1252I…

XP_011528619.1:p.Thr1252Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X4 XM_005261704.3:c.3755C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X2 XP_005261761.1:p.Thr1252I…

XP_005261761.1:p.Thr1252Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X5 XM_011530318.4:c.3677C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X3 XP_011528620.1:p.Thr1226I…

XP_011528620.1:p.Thr1226Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X6 XM_017028911.3:c.3833C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X4 XP_016884400.1:p.Thr1278I…

XP_016884400.1:p.Thr1278Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X7 XM_011530319.4:c.3437C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X5 XP_011528621.1:p.Thr1146I…

XP_011528621.1:p.Thr1146Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X8 XM_011530320.4:c.3833C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X6 XP_011528622.1:p.Thr1278I…

XP_011528622.1:p.Thr1278Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X10 XM_011530321.4:c.3299C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X7 XP_011528623.1:p.Thr1100I…

XP_011528623.1:p.Thr1100Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X11 XM_047441461.1:c.3299C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X7 XP_047297417.1:p.Thr1100I…

XP_047297417.1:p.Thr1100Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X12 XM_011530323.3:c.3293C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X8 XP_011528625.1:p.Thr1098I…

XP_011528625.1:p.Thr1098Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X13 XM_047441462.1:c.3281C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X9 XP_047297418.1:p.Thr1094I…

XP_047297418.1:p.Thr1094Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X14 XM_011530325.3:c.3011C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X10 XP_011528627.1:p.Thr1004I…

XP_011528627.1:p.Thr1004Ile

T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X16 XM_011530327.3:c.2831C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X12 XP_011528629.1:p.Thr944Ile T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X19 XM_047441464.1:c.1649C>T T [ACT] > I [ATT] Coding Sequence Variant
EF-hand calcium-binding domain-containing protein 6 isoform X15 XP_047297420.1:p.Thr550Ile T (Thr) > I (Ile) Missense Variant
EFCAB6 transcript variant X9 XR_007067980.1:n.4144C>T 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 G= A
GRCh38.p14 chr 22 NC_000022.11:g.43540251= NC_000022.11:g.43540251G>A
GRCh37.p13 chr 22 NC_000022.10:g.43936131= NC_000022.10:g.43936131G>A
EFCAB6 RefSeqGene NG_030019.1:g.277087= NG_030019.1:g.277087C>T
EFCAB6 transcript variant 1 NM_022785.4:c.3755= NM_022785.4:c.3755C>T
EFCAB6 transcript variant 1 NM_022785.3:c.3755= NM_022785.3:c.3755C>T
EFCAB6 transcript variant 2 NM_198856.3:c.3299= NM_198856.3:c.3299C>T
EFCAB6 transcript variant 2 NM_198856.2:c.3299= NM_198856.2:c.3299C>T
EFCAB6 transcript variant X5 XM_011530318.4:c.3677= XM_011530318.4:c.3677C>T
EFCAB6 transcript variant X5 XM_011530318.3:c.3677= XM_011530318.3:c.3677C>T
EFCAB6 transcript variant X5 XM_011530318.2:c.3677= XM_011530318.2:c.3677C>T
EFCAB6 transcript variant X4 XM_011530318.1:c.3677= XM_011530318.1:c.3677C>T
EFCAB6 transcript variant X3 XM_011530317.4:c.3755= XM_011530317.4:c.3755C>T
EFCAB6 transcript variant X4 XM_011530317.3:c.3755= XM_011530317.3:c.3755C>T
EFCAB6 transcript variant X4 XM_011530317.2:c.3755= XM_011530317.2:c.3755C>T
EFCAB6 transcript variant X3 XM_011530317.1:c.3755= XM_011530317.1:c.3755C>T
EFCAB6 transcript variant X8 XM_011530320.4:c.3833= XM_011530320.4:c.3833C>T
EFCAB6 transcript variant X9 XM_011530320.3:c.3833= XM_011530320.3:c.3833C>T
EFCAB6 transcript variant X9 XM_011530320.2:c.3833= XM_011530320.2:c.3833C>T
EFCAB6 transcript variant X7 XM_011530320.1:c.3833= XM_011530320.1:c.3833C>T
EFCAB6 transcript variant X7 XM_011530319.4:c.3437= XM_011530319.4:c.3437C>T
EFCAB6 transcript variant X8 XM_011530319.3:c.3437= XM_011530319.3:c.3437C>T
EFCAB6 transcript variant X8 XM_011530319.2:c.3437= XM_011530319.2:c.3437C>T
EFCAB6 transcript variant X6 XM_011530319.1:c.3437= XM_011530319.1:c.3437C>T
EFCAB6 transcript variant X10 XM_011530321.4:c.3299= XM_011530321.4:c.3299C>T
EFCAB6 transcript variant X13 XM_011530321.3:c.3299= XM_011530321.3:c.3299C>T
EFCAB6 transcript variant X12 XM_011530321.2:c.3299= XM_011530321.2:c.3299C>T
EFCAB6 transcript variant X10 XM_011530321.1:c.3299= XM_011530321.1:c.3299C>T
EFCAB6 transcript variant X1 XM_017028910.3:c.3833= XM_017028910.3:c.3833C>T
EFCAB6 transcript variant X1 XM_017028910.2:c.3833= XM_017028910.2:c.3833C>T
EFCAB6 transcript variant X1 XM_017028910.1:c.3833= XM_017028910.1:c.3833C>T
EFCAB6 transcript variant X4 XM_005261704.3:c.3755= XM_005261704.3:c.3755C>T
EFCAB6 transcript variant X3 XM_005261704.2:c.3755= XM_005261704.2:c.3755C>T
EFCAB6 transcript variant X1 XM_005261704.1:c.3755= XM_005261704.1:c.3755C>T
EFCAB6 transcript variant X6 XM_017028911.3:c.3833= XM_017028911.3:c.3833C>T
EFCAB6 transcript variant X6 XM_017028911.2:c.3833= XM_017028911.2:c.3833C>T
EFCAB6 transcript variant X6 XM_017028911.1:c.3833= XM_017028911.1:c.3833C>T
EFCAB6 transcript variant X12 XM_011530323.3:c.3293= XM_011530323.3:c.3293C>T
EFCAB6 transcript variant X14 XM_011530323.2:c.3293= XM_011530323.2:c.3293C>T
EFCAB6 transcript variant X12 XM_011530323.1:c.3293= XM_011530323.1:c.3293C>T
EFCAB6 transcript variant X14 XM_011530325.3:c.3011= XM_011530325.3:c.3011C>T
EFCAB6 transcript variant X16 XM_011530325.2:c.3011= XM_011530325.2:c.3011C>T
EFCAB6 transcript variant X14 XM_011530325.1:c.3011= XM_011530325.1:c.3011C>T
EFCAB6 transcript variant X16 XM_011530327.3:c.2831= XM_011530327.3:c.2831C>T
EFCAB6 transcript variant X18 XM_011530327.2:c.2831= XM_011530327.2:c.2831C>T
EFCAB6 transcript variant X16 XM_011530327.1:c.2831= XM_011530327.1:c.2831C>T
EFCAB6 transcript variant X2 XM_011530316.2:c.3833= XM_011530316.2:c.3833C>T
EFCAB6 transcript variant X2 XM_011530316.1:c.3833= XM_011530316.1:c.3833C>T
EFCAB6 transcript variant X11 XM_047441461.1:c.3299= XM_047441461.1:c.3299C>T
EFCAB6 transcript variant X9 XR_007067980.1:n.4144= XR_007067980.1:n.4144C>T
EFCAB6 transcript variant X13 XM_047441462.1:c.3281= XM_047441462.1:c.3281C>T
EFCAB6 transcript variant X19 XM_047441464.1:c.1649= XM_047441464.1:c.1649C>T
EF-hand calcium-binding domain-containing protein 6 isoform a NP_073622.2:p.Thr1252= NP_073622.2:p.Thr1252Ile
EF-hand calcium-binding domain-containing protein 6 isoform b NP_942153.1:p.Thr1100= NP_942153.1:p.Thr1100Ile
EF-hand calcium-binding domain-containing protein 6 isoform X3 XP_011528620.1:p.Thr1226= XP_011528620.1:p.Thr1226Ile
EF-hand calcium-binding domain-containing protein 6 isoform X2 XP_011528619.1:p.Thr1252= XP_011528619.1:p.Thr1252Ile
EF-hand calcium-binding domain-containing protein 6 isoform X6 XP_011528622.1:p.Thr1278= XP_011528622.1:p.Thr1278Ile
EF-hand calcium-binding domain-containing protein 6 isoform X5 XP_011528621.1:p.Thr1146= XP_011528621.1:p.Thr1146Ile
EF-hand calcium-binding domain-containing protein 6 isoform X7 XP_011528623.1:p.Thr1100= XP_011528623.1:p.Thr1100Ile
EF-hand calcium-binding domain-containing protein 6 isoform X1 XP_016884399.1:p.Thr1278= XP_016884399.1:p.Thr1278Ile
EF-hand calcium-binding domain-containing protein 6 isoform X2 XP_005261761.1:p.Thr1252= XP_005261761.1:p.Thr1252Ile
EF-hand calcium-binding domain-containing protein 6 isoform X4 XP_016884400.1:p.Thr1278= XP_016884400.1:p.Thr1278Ile
EF-hand calcium-binding domain-containing protein 6 isoform X8 XP_011528625.1:p.Thr1098= XP_011528625.1:p.Thr1098Ile
EF-hand calcium-binding domain-containing protein 6 isoform X10 XP_011528627.1:p.Thr1004= XP_011528627.1:p.Thr1004Ile
EF-hand calcium-binding domain-containing protein 6 isoform X12 XP_011528629.1:p.Thr944= XP_011528629.1:p.Thr944Ile
EF-hand calcium-binding domain-containing protein 6 isoform X1 XP_011528618.1:p.Thr1278= XP_011528618.1:p.Thr1278Ile
EF-hand calcium-binding domain-containing protein 6 isoform X7 XP_047297417.1:p.Thr1100= XP_047297417.1:p.Thr1100Ile
EF-hand calcium-binding domain-containing protein 6 isoform X9 XP_047297418.1:p.Thr1094= XP_047297418.1:p.Thr1094Ile
EF-hand calcium-binding domain-containing protein 6 isoform X15 XP_047297420.1:p.Thr550= XP_047297420.1:p.Thr550Ile
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, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2745206441 Nov 08, 2017 (151)
2 TOPMED ss5111175243 Apr 27, 2021 (155)
3 gnomAD - Exomes NC_000022.10 - 43936131 Jul 13, 2019 (153)
4 TopMed NC_000022.11 - 43540251 Apr 27, 2021 (155)
5 ALFA NC_000022.11 - 43540251 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
14539683, ss2745206441 NC_000022.10:43936130:G:A NC_000022.11:43540250:G:A (self)
386284190, 2934946166, ss5111175243 NC_000022.11:43540250:G:A NC_000022.11:43540250:G:A (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 rs1476170948

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