Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs1439861535

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:158182166 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
T=0.000004 (1/251464, GnomAD_exome)
T=0.00004 (1/28256, 14KJPN) (+ 2 more)
T=0.00005 (1/19668, ALFA)
T=0.00006 (1/16760, 8.3KJPN)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CD1D : 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 19668 G=0.99995 A=0.00000, T=0.00005 0.999898 0.0 0.000102 0
European Sub 13024 G=1.00000 A=0.00000, T=0.00000 1.0 0.0 0.0 N/A
African Sub 2888 G=1.0000 A=0.0000, T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 92 G=1.00 A=0.00, T=0.00 1.0 0.0 0.0 N/A
African American Sub 2796 G=1.0000 A=0.0000, T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 164 G=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 110 G=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 54 G=1.00 A=0.00, T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000, T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 A=0.00, T=0.00 1.0 0.0 0.0 N/A
Other Sub 2742 G=0.9996 A=0.0000, T=0.0004 0.999271 0.0 0.000729 0


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=0.999996 A=0.000004
gnomAD - Exomes Global Study-wide 251464 G=0.999996 T=0.000004
gnomAD - Exomes European Sub 135404 G=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 49010 G=1.00000 T=0.00000
gnomAD - Exomes American Sub 34590 G=1.00000 T=0.00000
gnomAD - Exomes African Sub 16246 G=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10074 G=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6140 G=0.9998 T=0.0002
14KJPN JAPANESE Study-wide 28256 G=0.99996 T=0.00004
Allele Frequency Aggregator Total Global 19668 G=0.99995 A=0.00000, T=0.00005
Allele Frequency Aggregator European Sub 13024 G=1.00000 A=0.00000, T=0.00000
Allele Frequency Aggregator African Sub 2888 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 2742 G=0.9996 A=0.0000, T=0.0004
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 164 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00, T=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.99994 T=0.00006
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 1 NC_000001.11:g.158182166G>A
GRCh38.p14 chr 1 NC_000001.11:g.158182166G>T
GRCh37.p13 chr 1 NC_000001.10:g.158151956G>A
GRCh37.p13 chr 1 NC_000001.10:g.158151956G>T
Gene: CD1D, CD1d molecule (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CD1D transcript variant 3 NM_001371761.1:c.151G>A A [GCC] > T [ACC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform 3 NP_001358690.1:p.Ala51Thr A (Ala) > T (Thr) Missense Variant
CD1D transcript variant 3 NM_001371761.1:c.151G>T A [GCC] > S [TCC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform 3 NP_001358690.1:p.Ala51Ser A (Ala) > S (Ser) Missense Variant
CD1D transcript variant 5 NM_001371763.1:c.463G>A A [GCC] > T [ACC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform 1 precursor NP_001358692.1:p.Ala155Thr A (Ala) > T (Thr) Missense Variant
CD1D transcript variant 5 NM_001371763.1:c.463G>T A [GCC] > S [TCC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform 1 precursor NP_001358692.1:p.Ala155Ser A (Ala) > S (Ser) Missense Variant
CD1D transcript variant 2 NM_001319145.2:c.463G>A A [GCC] > T [ACC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform 2 precursor NP_001306074.1:p.Ala155Thr A (Ala) > T (Thr) Missense Variant
CD1D transcript variant 2 NM_001319145.2:c.463G>T A [GCC] > S [TCC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform 2 precursor NP_001306074.1:p.Ala155Ser A (Ala) > S (Ser) Missense Variant
CD1D transcript variant 4 NM_001371762.2:c.463G>A A [GCC] > T [ACC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform 1 precursor NP_001358691.1:p.Ala155Thr A (Ala) > T (Thr) Missense Variant
CD1D transcript variant 4 NM_001371762.2:c.463G>T A [GCC] > S [TCC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform 1 precursor NP_001358691.1:p.Ala155Ser A (Ala) > S (Ser) Missense Variant
CD1D transcript variant 1 NM_001766.4:c.463G>A A [GCC] > T [ACC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform 1 precursor NP_001757.1:p.Ala155Thr A (Ala) > T (Thr) Missense Variant
CD1D transcript variant 1 NM_001766.4:c.463G>T A [GCC] > S [TCC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform 1 precursor NP_001757.1:p.Ala155Ser A (Ala) > S (Ser) Missense Variant
CD1D transcript variant X1 XM_047433945.1:c.463G>A A [GCC] > T [ACC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform X1 XP_047289901.1:p.Ala155Thr A (Ala) > T (Thr) Missense Variant
CD1D transcript variant X1 XM_047433945.1:c.463G>T A [GCC] > S [TCC] Coding Sequence Variant
antigen-presenting glycoprotein CD1d isoform X1 XP_047289901.1:p.Ala155Ser A (Ala) > S (Ser) Missense 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 T
GRCh38.p14 chr 1 NC_000001.11:g.158182166= NC_000001.11:g.158182166G>A NC_000001.11:g.158182166G>T
GRCh37.p13 chr 1 NC_000001.10:g.158151956= NC_000001.10:g.158151956G>A NC_000001.10:g.158151956G>T
CD1D transcript variant 1 NM_001766.4:c.463= NM_001766.4:c.463G>A NM_001766.4:c.463G>T
CD1D transcript variant 1 NM_001766.3:c.463= NM_001766.3:c.463G>A NM_001766.3:c.463G>T
CD1D transcript variant 4 NM_001371762.2:c.463= NM_001371762.2:c.463G>A NM_001371762.2:c.463G>T
CD1D transcript variant 4 NM_001371762.1:c.463= NM_001371762.1:c.463G>A NM_001371762.1:c.463G>T
CD1D transcript variant 2 NM_001319145.2:c.463= NM_001319145.2:c.463G>A NM_001319145.2:c.463G>T
CD1D transcript variant 2 NM_001319145.1:c.463= NM_001319145.1:c.463G>A NM_001319145.1:c.463G>T
CD1D transcript variant 5 NM_001371763.1:c.463= NM_001371763.1:c.463G>A NM_001371763.1:c.463G>T
CD1D transcript variant 3 NM_001371761.1:c.151= NM_001371761.1:c.151G>A NM_001371761.1:c.151G>T
CD1D transcript variant X1 XM_047433945.1:c.463= XM_047433945.1:c.463G>A XM_047433945.1:c.463G>T
antigen-presenting glycoprotein CD1d isoform 1 precursor NP_001757.1:p.Ala155= NP_001757.1:p.Ala155Thr NP_001757.1:p.Ala155Ser
antigen-presenting glycoprotein CD1d isoform 1 precursor NP_001358691.1:p.Ala155= NP_001358691.1:p.Ala155Thr NP_001358691.1:p.Ala155Ser
antigen-presenting glycoprotein CD1d isoform 2 precursor NP_001306074.1:p.Ala155= NP_001306074.1:p.Ala155Thr NP_001306074.1:p.Ala155Ser
antigen-presenting glycoprotein CD1d isoform 1 precursor NP_001358692.1:p.Ala155= NP_001358692.1:p.Ala155Thr NP_001358692.1:p.Ala155Ser
antigen-presenting glycoprotein CD1d isoform 3 NP_001358690.1:p.Ala51= NP_001358690.1:p.Ala51Thr NP_001358690.1:p.Ala51Ser
antigen-presenting glycoprotein CD1d isoform X1 XP_047289901.1:p.Ala155= XP_047289901.1:p.Ala155Thr XP_047289901.1:p.Ala155Ser
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#.

5 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2731963005 Nov 08, 2017 (151)
2 VINODS ss4018964429 Apr 25, 2021 (155)
3 TOPMED ss4469179172 Apr 25, 2021 (155)
4 TOMMO_GENOMICS ss5146599254 Apr 25, 2021 (155)
5 TOMMO_GENOMICS ss5673832757 Oct 12, 2022 (156)
6 gnomAD - Exomes NC_000001.10 - 158151956 Jul 12, 2019 (153)
7 8.3KJPN NC_000001.10 - 158151956 Apr 25, 2021 (155)
8 14KJPN NC_000001.11 - 158182166 Oct 12, 2022 (156)
9 TopMed NC_000001.11 - 158182166 Apr 25, 2021 (155)
10 ALFA NC_000001.11 - 158182166 Apr 25, 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
32785507, 3670036028, ss4469179172 NC_000001.11:158182165:G:A NC_000001.11:158182165:G:A (self)
987356, 4568561, ss2731963005, ss5146599254 NC_000001.10:158151955:G:T NC_000001.11:158182165:G:T (self)
7669861, 3670036028, ss4018964429, ss5673832757 NC_000001.11:158182165:G:T NC_000001.11:158182165:G: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 rs1439861535

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