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dbSNP Short Genetic Variations

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.

rs1050105

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr6:31269992 (GRCh38.p12) 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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.27470 (46478/169196, GnomAD)
G=0.3028 (9006/29738, GnomAD)
G=0.242 (1214/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HLA-C : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 6 NC_000006.12:g.31269992G>A
GRCh38.p12 chr 6 NC_000006.12:g.31269992G>C
GRCh38.p12 chr 6 NC_000006.12:g.31269992G>T
GRCh37.p13 chr 6 NC_000006.11:g.31237769G>A
GRCh37.p13 chr 6 NC_000006.11:g.31237769G>C
GRCh37.p13 chr 6 NC_000006.11:g.31237769G>T
HLA-C RefSeqGene NG_029422.2:g.7140C>T
HLA-C RefSeqGene NG_029422.2:g.7140C>G
HLA-C RefSeqGene NG_029422.2:g.7140C>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2750918G>A
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2750918G>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.2750918G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2751024G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2751024G>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.2751024G>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.2612719A>G
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.2612719A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.2612719A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.2618304A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.2618304A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.2618304A>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2579041A>G
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2579041A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.2579041A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2584661A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2584661A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.2584661A>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2527789A>G
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2527789A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.2527789A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2533374A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2533374A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.2533374A>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2571947A>G
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2571947A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.2571947A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2571245A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2571245A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.2571245A>T
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2525421A>G
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2525421A>C
GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.2525421A>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2531017A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2531017A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.2531017A>T
Gene: HLA-C, major histocompatibility complex, class I, C (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HLA-C transcript variant 1 NM_002117.5:c.989C>T A [GCT] > V [GTT] Coding Sequence Variant
HLA class I histocompatibility antigen, Cw-1 alpha chain precursor NP_002108.4:p.Ala330Val A (Ala) > V (Val) Missense Variant
HLA-C transcript variant 1 NM_002117.5:c.989C>G A [GCT] > G [GGT] Coding Sequence Variant
HLA class I histocompatibility antigen, Cw-1 alpha chain precursor NP_002108.4:p.Ala330Gly A (Ala) > G (Gly) Missense Variant
HLA-C transcript variant 1 NM_002117.5:c.989C>A A [GCT] > D [GAT] Coding Sequence Variant
HLA class I histocompatibility antigen, Cw-1 alpha chain precursor NP_002108.4:p.Ala330Asp A (Ala) > D (Asp) 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

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 - Exomes Global Study-wide 169196 G=0.27470 A=0.72530
gnomAD - Exomes European Sub 89712 G=0.3258 A=0.6742
gnomAD - Exomes Asian Sub 34144 G=0.2056 A=0.7944
gnomAD - Exomes American Sub 23662 G=0.2367 A=0.7633
gnomAD - Exomes African Sub 11484 G=0.2386 A=0.7614
gnomAD - Exomes Ashkenazi Jewish Sub 6402 G=0.143 A=0.857
gnomAD - Exomes Other Sub 3792 G=0.256 A=0.744
gnomAD - Genomes Global Study-wide 29738 G=0.3028 A=0.6972
gnomAD - Genomes European Sub 17752 G=0.3388 A=0.6612
gnomAD - Genomes African Sub 8394 G=0.250 A=0.750
gnomAD - Genomes East Asian Sub 1592 G=0.210 A=0.790
gnomAD - Genomes Other Sub 924 G=0.31 A=0.69
gnomAD - Genomes American Sub 808 G=0.28 A=0.72
gnomAD - Genomes Ashkenazi Jewish Sub 268 G=0.18 A=0.82
1000Genomes Global Study-wide 5008 G=0.242 A=0.758
1000Genomes African Sub 1322 G=0.267 A=0.733
1000Genomes East Asian Sub 1008 G=0.188 A=0.812
1000Genomes Europe Sub 1006 G=0.289 A=0.711
1000Genomes South Asian Sub 978 G=0.25 A=0.75
1000Genomes American Sub 694 G=0.20 A=0.80
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 C T Note
GRCh38.p12 chr 6 NC_000006.12:...

NC_000006.12:g.31269992G=

NC_000006.12:...

NC_000006.12:g.31269992G>A

NC_000006.12:...

NC_000006.12:g.31269992G>C

NC_000006.12:...

NC_000006.12:g.31269992G>T

GRCh37.p13 chr 6 NC_000006.11:...

NC_000006.11:g.31237769G=

NC_000006.11:...

NC_000006.11:g.31237769G>A

NC_000006.11:...

NC_000006.11:g.31237769G>C

NC_000006.11:...

NC_000006.11:g.31237769G>T

HLA-C RefSeqGene NG_029422.2:g...

NG_029422.2:g.7140C=

NG_029422.2:g...

NG_029422.2:g.7140C>T

NG_029422.2:g...

NG_029422.2:g.7140C>G

NG_029422.2:g...

NG_029422.2:g.7140C>A

HLA-C transcript variant 1 NM_002117.5:c...

NM_002117.5:c.989C=

NM_002117.5:c...

NM_002117.5:c.989C>T

NM_002117.5:c...

NM_002117.5:c.989C>G

NM_002117.5:c...

NM_002117.5:c.989C>A

HLA-C transcript variant 2 NM_001243042....

NM_001243042.1:c.989C=

NM_001243042....

NM_001243042.1:c.989C>T

NM_001243042....

NM_001243042.1:c.989C>G

NM_001243042....

NM_001243042.1:c.989C>A

GRCh38.p12 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g...

NT_113891.3:g.2750918G=

NT_113891.3:g...

NT_113891.3:g.2750918G>A

NT_113891.3:g...

NT_113891.3:g.2750918G>C

NT_113891.3:g...

NT_113891.3:g.2750918G>T

GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g...

NT_113891.2:g.2751024G=

NT_113891.2:g...

NT_113891.2:g.2751024G>A

NT_113891.2:g...

NT_113891.2:g.2751024G>C

NT_113891.2:g...

NT_113891.2:g.2751024G>T

GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g...

NT_167247.2:g.2612719A>G

NT_167247.2:g...

NT_167247.2:g.2612719A=

NT_167247.2:g...

NT_167247.2:g.2612719A>C

NT_167247.2:g...

NT_167247.2:g.2612719A>T

GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g...

NT_167247.1:g.2618304A>G

NT_167247.1:g...

NT_167247.1:g.2618304A=

NT_167247.1:g...

NT_167247.1:g.2618304A>C

NT_167247.1:g...

NT_167247.1:g.2618304A>T

GRCh38.p12 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g...

NT_167246.2:g.2579041A>G

NT_167246.2:g...

NT_167246.2:g.2579041A=

NT_167246.2:g...

NT_167246.2:g.2579041A>C

NT_167246.2:g...

NT_167246.2:g.2579041A>T

GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g...

NT_167246.1:g.2584661A>G

NT_167246.1:g...

NT_167246.1:g.2584661A=

NT_167246.1:g...

NT_167246.1:g.2584661A>C

NT_167246.1:g...

NT_167246.1:g.2584661A>T

GRCh38.p12 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g...

NT_167245.2:g.2527789A>G

NT_167245.2:g...

NT_167245.2:g.2527789A=

NT_167245.2:g...

NT_167245.2:g.2527789A>C

NT_167245.2:g...

NT_167245.2:g.2527789A>T

GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g...

NT_167245.1:g.2533374A>G

NT_167245.1:g...

NT_167245.1:g.2533374A=

NT_167245.1:g...

NT_167245.1:g.2533374A>C

NT_167245.1:g...

NT_167245.1:g.2533374A>T

GRCh38.p12 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g...

NT_167249.2:g.2571947A>G

NT_167249.2:g...

NT_167249.2:g.2571947A=

NT_167249.2:g...

NT_167249.2:g.2571947A>C

NT_167249.2:g...

NT_167249.2:g.2571947A>T

GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g...

NT_167249.1:g.2571245A>G

NT_167249.1:g...

NT_167249.1:g.2571245A=

NT_167249.1:g...

NT_167249.1:g.2571245A>C

NT_167249.1:g...

NT_167249.1:g.2571245A>T

GRCh38.p12 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g...

NT_167248.2:g.2525421A>G

NT_167248.2:g...

NT_167248.2:g.2525421A=

NT_167248.2:g...

NT_167248.2:g.2525421A>C

NT_167248.2:g...

NT_167248.2:g.2525421A>T

GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g...

NT_167248.1:g.2531017A>G

NT_167248.1:g...

NT_167248.1:g.2531017A=

NT_167248.1:g...

NT_167248.1:g.2531017A>C

NT_167248.1:g...

NT_167248.1:g.2531017A>T

HLA class I histocompatibility antigen, Cw-1 alpha chain precursor NP_002108.4:p...

NP_002108.4:p.Ala330=

NP_002108.4:p...

NP_002108.4:p.Ala330Val

NP_002108.4:p...

NP_002108.4:p.Ala330Gly

NP_002108.4:p...

NP_002108.4:p.Ala330Asp

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#.

24 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 LEE ss1524424 Oct 05, 2000 (86)
2 LEE ss4394379 May 29, 2002 (130)
3 LEE ss4415320 May 29, 2002 (108)
4 SI_MHC_SNP ss12687873 Oct 31, 2003 (130)
5 SEQUENOM ss24796269 Sep 21, 2004 (123)
6 HUMANGENOME_JCVI ss98378552 Feb 06, 2009 (130)
7 EXOME_CHIP ss491381447 May 04, 2012 (137)
8 CLINSEQ_SNP ss491884658 May 04, 2012 (137)
9 DBMHC ss539004457 Sep 21, 2012 (137)
10 SSMP ss653029029 Apr 25, 2013 (138)
11 1000GENOMES ss1319545519 Aug 21, 2014 (142)
12 EVA_EXAC ss1688227651 Apr 01, 2015 (144)
13 EVA_EXAC ss1688227652 Apr 01, 2015 (144)
14 WEILL_CORNELL_DGM ss1926009939 Feb 12, 2016 (147)
15 JJLAB ss2023635910 Sep 14, 2016 (149)
16 USC_VALOUEV ss2151801547 Nov 08, 2017 (151)
17 GRF ss2707394562 Nov 08, 2017 (151)
18 GNOMAD ss2735644570 Nov 08, 2017 (151)
19 GNOMAD ss2747580224 Nov 08, 2017 (151)
20 GNOMAD ss2837400072 Nov 08, 2017 (151)
21 SWEGEN ss2998785531 Nov 08, 2017 (151)
22 TOPMED ss3493788777 Nov 08, 2017 (151)
23 OMUKHERJEE_ADBS ss3646334132 Oct 12, 2018 (152)
24 URBANLAB ss3648307456 Oct 12, 2018 (152)
25 1000Genomes NC_000006.11 - 31237769 Oct 12, 2018 (152)
26 ExAC

Submission ignored due to conflicting rows:
Row 8252521 (NC_000006.11:31237768:G:G 38001/114230, NC_000006.11:31237768:G:A 76229/114230)
Row 8252522 (NC_000006.11:31237768:G:G 114229/114230, NC_000006.11:31237768:G:C 1/114230)

- Oct 12, 2018 (152)
27 ExAC

Submission ignored due to conflicting rows:
Row 8252521 (NC_000006.11:31237768:G:G 38001/114230, NC_000006.11:31237768:G:A 76229/114230)
Row 8252522 (NC_000006.11:31237768:G:G 114229/114230, NC_000006.11:31237768:G:C 1/114230)

- Oct 12, 2018 (152)
28 gnomAD - Genomes NC_000006.11 - 31237769 Oct 12, 2018 (152)
29 gnomAD - Exomes NC_000006.11 - 31237769 Oct 12, 2018 (152)
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).

Associated ID History Updated (Build)
rs2308647 May 26, 2008 (130)
rs3177837 Oct 08, 2004 (123)
rs3190386 Oct 09, 2002 (108)
rs9264613 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss491884658 NC_000006.10:31345747:G:A NC_000006.12:31269991:G:A (self)
31312411, 178027829, 3812367, ss491381447, ss653029029, ss1319545519, ss1688227651, ss1926009939, ss2023635910, ss2151801547, ss2707394562, ss2735644570, ss2747580224, ss2837400072, ss2998785531, ss3646334132 NC_000006.11:31237768:G:A NC_000006.12:31269991:G:A (self)
ss539004457, ss3493788777, ss3648307456 NC_000006.12:31269991:G:A NC_000006.12:31269991:G:A (self)
ss1524424, ss4394379, ss4415320, ss12687873, ss24796269 NT_007592.15:31177768:G:A NC_000006.12:31269991:G:A (self)
ss1688227652 NC_000006.11:31237768:G:C NC_000006.12:31269991:G:C (self)
ss98378552 NT_007592.15:31177768:G:C NC_000006.12:31269991:G:C (self)
ss98378552 NT_007592.15:31177768:G:T NC_000006.12:31269991: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 rs1050105

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.post104+4a6ee9c