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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1474890989

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:21161240 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000008 (2/264690, TOPMED)
T=0.000014 (2/140310, GnomAD)
T=0.00007 (1/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LDAF1 : Synonymous Variant
DNAH3 : 2KB Upstream 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 14050 C=0.99993 T=0.00007 0.999858 0.0 0.000142 0
European Sub 9690 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 C=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 C=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=0.998 T=0.002 0.996721 0.0 0.003279 0
South Asian Sub 98 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 496 C=1.000 T=0.000 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 C=0.999992 T=0.000008
gnomAD - Genomes Global Study-wide 140310 C=0.999986 T=0.000014
gnomAD - Genomes European Sub 75976 C=0.99997 T=0.00003
gnomAD - Genomes African Sub 42060 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13662 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 14050 C=0.99993 T=0.00007
Allele Frequency Aggregator European Sub 9690 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2898 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.998 T=0.002
Allele Frequency Aggregator Other Sub 496 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=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 16 NC_000016.10:g.21161240C>T
GRCh37.p13 chr 16 NC_000016.9:g.21172561C>T
DNAH3 RefSeqGene NG_052617.1:g.3202G>A
Gene: DNAH3, dynein axonemal heavy chain 3 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
DNAH3 transcript variant 1 NM_017539.2:c. N/A Upstream Transcript Variant
DNAH3 transcript variant 2 NM_001347886.2:c. N/A N/A
DNAH3 transcript variant 3 NM_001394581.1:c. N/A N/A
DNAH3 transcript variant X15 XM_017023432.2:c. N/A Upstream Transcript Variant
DNAH3 transcript variant X1 XM_011545882.3:c. N/A N/A
DNAH3 transcript variant X2 XM_011545883.1:c. N/A N/A
DNAH3 transcript variant X8 XM_011545885.4:c. N/A N/A
DNAH3 transcript variant X9 XM_011545886.3:c. N/A N/A
DNAH3 transcript variant X10 XM_011545888.2:c. N/A N/A
DNAH3 transcript variant X11 XM_011545889.2:c. N/A N/A
DNAH3 transcript variant X4 XM_017023426.2:c. N/A N/A
DNAH3 transcript variant X5 XM_017023427.2:c. N/A N/A
DNAH3 transcript variant X7 XM_017023428.2:c. N/A N/A
DNAH3 transcript variant X12 XM_017023429.2:c. N/A N/A
DNAH3 transcript variant X13 XM_017023430.2:c. N/A N/A
DNAH3 transcript variant X14 XM_017023431.2:c. N/A N/A
DNAH3 transcript variant X3 XM_047434348.1:c. N/A N/A
DNAH3 transcript variant X6 XM_047434349.1:c. N/A N/A
Gene: LDAF1, lipid droplet assembly factor 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LDAF1 transcript variant 6 NM_001301774.2:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform 3 NP_001288703.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant 3 NM_001301769.2:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform 2 NP_001288698.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant 5 NM_001301773.2:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform 3 NP_001288702.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant 2 NM_020422.6:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform 2 NP_065155.3:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant 4 NM_001301771.2:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform 2 NP_001288700.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant 1 NM_001301775.2:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform 1 NP_001288704.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant 7 NR_125971.2:n.229C>T N/A Non Coding Transcript Variant
LDAF1 transcript variant X1 XM_006721066.3:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform X8 XP_006721129.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant X2 XM_017023471.2:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform X1 XP_016878960.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant X3 XM_047434368.1:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform X2 XP_047290324.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant X4 XM_006721067.5:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform X3 XP_006721130.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant X5 XM_047434369.1:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform X4 XP_047290325.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant X6 XM_017023473.3:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform X4 XP_016878962.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant X7 XM_017023474.2:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform X5 XP_016878963.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant X8 XM_047434370.1:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform X5 XP_047290326.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant X9 XM_024450356.2:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform X6 XP_024306124.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant X10 XM_024450357.2:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform X6 XP_024306125.1:p.Leu20= L (Leu) > L (Leu) Synonymous Variant
LDAF1 transcript variant X11 XM_006721069.4:c.58C>T L [CTG] > L [TTG] Coding Sequence Variant
lipid droplet assembly factor 1 isoform X7 XP_006721132.1:p.Leu20= L (Leu) > L (Leu) Synonymous 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 C= T
GRCh38.p14 chr 16 NC_000016.10:g.21161240= NC_000016.10:g.21161240C>T
GRCh37.p13 chr 16 NC_000016.9:g.21172561= NC_000016.9:g.21172561C>T
DNAH3 RefSeqGene NG_052617.1:g.3202= NG_052617.1:g.3202G>A
LDAF1 transcript variant 2 NM_020422.6:c.58= NM_020422.6:c.58C>T
TMEM159 transcript variant 2 NM_020422.5:c.58= NM_020422.5:c.58C>T
TMEM159 transcript NM_020422.4:c.58= NM_020422.4:c.58C>T
LDAF1 transcript variant X4 XM_006721067.5:c.58= XM_006721067.5:c.58C>T
LDAF1 transcript variant X5 XM_006721067.4:c.58= XM_006721067.4:c.58C>T
TMEM159 transcript variant X5 XM_006721067.3:c.58= XM_006721067.3:c.58C>T
TMEM159 transcript variant X3 XM_006721067.2:c.58= XM_006721067.2:c.58C>T
TMEM159 transcript variant X5 XM_006721067.1:c.58= XM_006721067.1:c.58C>T
LDAF1 transcript variant X11 XM_006721069.4:c.58= XM_006721069.4:c.58C>T
LDAF1 transcript variant X11 XM_006721069.3:c.58= XM_006721069.3:c.58C>T
TMEM159 transcript variant X4 XM_006721069.2:c.58= XM_006721069.2:c.58C>T
TMEM159 transcript variant X7 XM_006721069.1:c.58= XM_006721069.1:c.58C>T
LDAF1 transcript variant X6 XM_017023473.3:c.58= XM_017023473.3:c.58C>T
LDAF1 transcript variant X6 XM_017023473.2:c.58= XM_017023473.2:c.58C>T
TMEM159 transcript variant X6 XM_017023473.1:c.58= XM_017023473.1:c.58C>T
LDAF1 transcript variant X1 XM_006721066.3:c.58= XM_006721066.3:c.58C>T
LDAF1 transcript variant X1 XM_006721066.2:c.58= XM_006721066.2:c.58C>T
TMEM159 transcript variant X1 XM_006721066.1:c.58= XM_006721066.1:c.58C>T
LDAF1 transcript variant X2 XM_017023471.2:c.58= XM_017023471.2:c.58C>T
LDAF1 transcript variant X3 XM_017023471.1:c.58= XM_017023471.1:c.58C>T
LDAF1 transcript variant X7 XM_017023474.2:c.58= XM_017023474.2:c.58C>T
LDAF1 transcript variant X8 XM_017023474.1:c.58= XM_017023474.1:c.58C>T
LDAF1 transcript variant 7 NR_125971.2:n.229= NR_125971.2:n.229C>T
TMEM159 transcript variant 7 NR_125971.1:n.526= NR_125971.1:n.526C>T
LDAF1 transcript variant 1 NM_001301775.2:c.58= NM_001301775.2:c.58C>T
TMEM159 transcript variant 1 NM_001301775.1:c.58= NM_001301775.1:c.58C>T
LDAF1 transcript variant 3 NM_001301769.2:c.58= NM_001301769.2:c.58C>T
TMEM159 transcript variant 3 NM_001301769.1:c.58= NM_001301769.1:c.58C>T
LDAF1 transcript variant 4 NM_001301771.2:c.58= NM_001301771.2:c.58C>T
TMEM159 transcript variant 4 NM_001301771.1:c.58= NM_001301771.1:c.58C>T
LDAF1 transcript variant 5 NM_001301773.2:c.58= NM_001301773.2:c.58C>T
TMEM159 transcript variant 5 NM_001301773.1:c.58= NM_001301773.1:c.58C>T
LDAF1 transcript variant 6 NM_001301774.2:c.58= NM_001301774.2:c.58C>T
TMEM159 transcript variant 6 NM_001301774.1:c.58= NM_001301774.1:c.58C>T
LDAF1 transcript variant X9 XM_024450356.2:c.58= XM_024450356.2:c.58C>T
LDAF1 transcript variant X9 XM_024450356.1:c.58= XM_024450356.1:c.58C>T
LDAF1 transcript variant X10 XM_024450357.2:c.58= XM_024450357.2:c.58C>T
LDAF1 transcript variant X10 XM_024450357.1:c.58= XM_024450357.1:c.58C>T
LDAF1 transcript variant X8 XM_047434370.1:c.58= XM_047434370.1:c.58C>T
LDAF1 transcript variant X3 XM_047434368.1:c.58= XM_047434368.1:c.58C>T
LDAF1 transcript variant X5 XM_047434369.1:c.58= XM_047434369.1:c.58C>T
lipid droplet assembly factor 1 isoform 2 NP_065155.3:p.Leu20= NP_065155.3:p.Leu20=
lipid droplet assembly factor 1 isoform X3 XP_006721130.1:p.Leu20= XP_006721130.1:p.Leu20=
lipid droplet assembly factor 1 isoform X7 XP_006721132.1:p.Leu20= XP_006721132.1:p.Leu20=
lipid droplet assembly factor 1 isoform X4 XP_016878962.1:p.Leu20= XP_016878962.1:p.Leu20=
lipid droplet assembly factor 1 isoform X8 XP_006721129.1:p.Leu20= XP_006721129.1:p.Leu20=
lipid droplet assembly factor 1 isoform X1 XP_016878960.1:p.Leu20= XP_016878960.1:p.Leu20=
lipid droplet assembly factor 1 isoform X5 XP_016878963.1:p.Leu20= XP_016878963.1:p.Leu20=
lipid droplet assembly factor 1 isoform 1 NP_001288704.1:p.Leu20= NP_001288704.1:p.Leu20=
lipid droplet assembly factor 1 isoform 2 NP_001288698.1:p.Leu20= NP_001288698.1:p.Leu20=
lipid droplet assembly factor 1 isoform 2 NP_001288700.1:p.Leu20= NP_001288700.1:p.Leu20=
lipid droplet assembly factor 1 isoform 3 NP_001288702.1:p.Leu20= NP_001288702.1:p.Leu20=
lipid droplet assembly factor 1 isoform 3 NP_001288703.1:p.Leu20= NP_001288703.1:p.Leu20=
lipid droplet assembly factor 1 isoform X6 XP_024306124.1:p.Leu20= XP_024306124.1:p.Leu20=
lipid droplet assembly factor 1 isoform X6 XP_024306125.1:p.Leu20= XP_024306125.1:p.Leu20=
lipid droplet assembly factor 1 isoform X5 XP_047290326.1:p.Leu20= XP_047290326.1:p.Leu20=
lipid droplet assembly factor 1 isoform X2 XP_047290324.1:p.Leu20= XP_047290324.1:p.Leu20=
lipid droplet assembly factor 1 isoform X4 XP_047290325.1:p.Leu20= XP_047290325.1:p.Leu20=
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 ss4298343004 Apr 27, 2021 (155)
2 TOPMED ss5010622659 Apr 27, 2021 (155)
3 gnomAD - Genomes NC_000016.10 - 21161240 Apr 27, 2021 (155)
4 TopMed NC_000016.10 - 21161240 Apr 27, 2021 (155)
5 ALFA NC_000016.10 - 21161240 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
485322129, 226168320, 6859519337, ss4298343004, ss5010622659 NC_000016.10:21161239:C:T NC_000016.10:21161239:C:T (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 rs1474890989

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