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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.

rs777214281

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr12:21486512 (GRCh38.p13) 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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000132 (35/264690, TOPMED)
C=0.000179 (44/245286, GnomAD_exome)
C=0.000129 (18/139776, GnomAD) (+ 2 more)
C=0.000142 (17/119540, ExAC)
C=0.00009 (4/44420, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
RECQL : 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.p13 chr 12 NC_000012.12:g.21486512A>C
GRCh37.p13 chr 12 NC_000012.11:g.21639446A>C
Gene: RECQL, RecQ like helicase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RECQL transcript variant 1 NM_002907.4:c.468T>G I [ATT] > M [ATG] Coding Sequence Variant
ATP-dependent DNA helicase Q1 NP_002898.2:p.Ile156Met I (Ile) > M (Met) Missense Variant
RECQL transcript variant 2 NM_032941.3:c.468T>G I [ATT] > M [ATG] Coding Sequence Variant
ATP-dependent DNA helicase Q1 NP_116559.1:p.Ile156Met I (Ile) > M (Met) Missense Variant
RECQL transcript variant X2 XM_005253461.3:c.468T>G I [ATT] > M [ATG] Coding Sequence Variant
ATP-dependent DNA helicase Q1 isoform X1 XP_005253518.1:p.Ile156Met I (Ile) > M (Met) Missense Variant
RECQL transcript variant X1 XM_005253464.4:c.468T>G I [ATT] > M [ATG] Coding Sequence Variant
ATP-dependent DNA helicase Q1 isoform X1 XP_005253521.1:p.Ile156Met I (Ile) > M (Met) Missense Variant
RECQL transcript variant X3 XM_005253463.4:c.468T>G I [ATT] > M [ATG] Coding Sequence Variant
ATP-dependent DNA helicase Q1 isoform X1 XP_005253520.1:p.Ile156Met I (Ile) > M (Met) Missense Variant
RECQL transcript variant X4 XM_005253462.5:c.468T>G I [ATT] > M [ATG] Coding Sequence Variant
ATP-dependent DNA helicase Q1 isoform X1 XP_005253519.1:p.Ile156Met I (Ile) > M (Met) 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.

Allele: C (allele ID: 575883 )
ClinVar Accession Disease Names Clinical Significance
RCV000709218.1 Hereditary cancer-predisposing syndrome Uncertain-Significance
RCV001230378.2 not provided Uncertain-Significance

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 44420 A=0.99991 C=0.00009
European Sub 32650 A=0.99991 C=0.00009
African Sub 3512 A=1.0000 C=0.0000
African Others Sub 122 A=1.000 C=0.000
African American Sub 3390 A=1.0000 C=0.0000
Asian Sub 168 A=1.000 C=0.000
East Asian Sub 112 A=1.000 C=0.000
Other Asian Sub 56 A=1.00 C=0.00
Latin American 1 Sub 500 A=1.000 C=0.000
Latin American 2 Sub 628 A=1.000 C=0.000
South Asian Sub 98 A=1.00 C=0.00
Other Sub 6864 A=0.9999 C=0.0001


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 A=0.999868 C=0.000132
gnomAD - Exomes Global Study-wide 245286 A=0.999821 C=0.000179
gnomAD - Exomes European Sub 133536 A=0.999715 C=0.000285
gnomAD - Exomes Asian Sub 46428 A=1.00000 C=0.00000
gnomAD - Exomes American Sub 33318 A=0.99988 C=0.00012
gnomAD - Exomes African Sub 16102 A=0.99994 C=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 9926 A=1.0000 C=0.0000
gnomAD - Exomes Other Sub 5976 A=0.9998 C=0.0002
gnomAD - Genomes Global Study-wide 139776 A=0.999871 C=0.000129
gnomAD - Genomes European Sub 75640 A=0.99984 C=0.00016
gnomAD - Genomes African Sub 41936 A=0.99993 C=0.00007
gnomAD - Genomes American Sub 13602 A=0.99985 C=0.00015
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3130 A=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2148 A=0.9995 C=0.0005
ExAC Global Study-wide 119540 A=0.999858 C=0.000142
ExAC Europe Sub 72162 A=0.99978 C=0.00022
ExAC Asian Sub 24894 A=1.00000 C=0.00000
ExAC American Sub 11426 A=1.00000 C=0.00000
ExAC African Sub 10166 A=0.99990 C=0.00010
ExAC Other Sub 892 A=1.000 C=0.000
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 A= C
GRCh38.p13 chr 12 NC_000012.12:g.21486512= NC_000012.12:g.21486512A>C
GRCh37.p13 chr 12 NC_000012.11:g.21639446= NC_000012.11:g.21639446A>C
RECQL transcript variant X4 XM_005253462.5:c.468= XM_005253462.5:c.468T>G
RECQL transcript variant X2 XM_005253462.1:c.468= XM_005253462.1:c.468T>G
RECQL transcript variant 1 NM_002907.4:c.468= NM_002907.4:c.468T>G
RECQL transcript variant 1 NM_002907.3:c.468= NM_002907.3:c.468T>G
RECQL transcript variant X3 XM_005253463.4:c.468= XM_005253463.4:c.468T>G
RECQL transcript variant X3 XM_005253463.1:c.468= XM_005253463.1:c.468T>G
RECQL transcript variant X1 XM_005253464.4:c.468= XM_005253464.4:c.468T>G
RECQL transcript variant X4 XM_005253464.1:c.468= XM_005253464.1:c.468T>G
RECQL transcript variant X2 XM_005253461.3:c.468= XM_005253461.3:c.468T>G
RECQL transcript variant X1 XM_005253461.1:c.468= XM_005253461.1:c.468T>G
RECQL transcript variant 2 NM_032941.3:c.468= NM_032941.3:c.468T>G
RECQL transcript variant 2 NM_032941.2:c.468= NM_032941.2:c.468T>G
ATP-dependent DNA helicase Q1 isoform X1 XP_005253519.1:p.Ile156= XP_005253519.1:p.Ile156Met
ATP-dependent DNA helicase Q1 NP_002898.2:p.Ile156= NP_002898.2:p.Ile156Met
ATP-dependent DNA helicase Q1 isoform X1 XP_005253520.1:p.Ile156= XP_005253520.1:p.Ile156Met
ATP-dependent DNA helicase Q1 isoform X1 XP_005253521.1:p.Ile156= XP_005253521.1:p.Ile156Met
ATP-dependent DNA helicase Q1 isoform X1 XP_005253518.1:p.Ile156= XP_005253518.1:p.Ile156Met
ATP-dependent DNA helicase Q1 NP_116559.1:p.Ile156= NP_116559.1:p.Ile156Met
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#.

8 SubSNP, 5 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1690821747 Apr 01, 2015 (144)
2 HUMAN_LONGEVITY ss2188392441 Dec 20, 2016 (150)
3 TOPMED ss2352050544 Dec 20, 2016 (150)
4 GNOMAD ss2739678841 Nov 08, 2017 (151)
5 GNOMAD ss2748827143 Nov 08, 2017 (151)
6 GNOMAD ss2908200555 Nov 08, 2017 (151)
7 TOPMED ss3164926940 Nov 08, 2017 (151)
8 TOPMED ss4911283184 Apr 26, 2021 (155)
9 ExAC NC_000012.11 - 21639446 Oct 12, 2018 (152)
10 gnomAD - Genomes NC_000012.12 - 21486512 Apr 26, 2021 (155)
11 gnomAD - Exomes NC_000012.11 - 21639446 Jul 13, 2019 (153)
12 TopMed NC_000012.12 - 21486512 Apr 26, 2021 (155)
13 ALFA NC_000012.12 - 21486512 Apr 26, 2021 (155)
14 ClinVar RCV000709218.1 Jul 13, 2019 (153)
15 ClinVar RCV001230378.2 Apr 26, 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
1111963, 8906925, ss1690821747, ss2352050544, ss2739678841, ss2748827143, ss2908200555 NC_000012.11:21639445:A:C NC_000012.12:21486511:A:C (self)
RCV000709218.1, RCV001230378.2, 401442768, 79470517, 126828841, 10974241445, ss2188392441, ss3164926940, ss4911283184 NC_000012.12:21486511:A:C NC_000012.12:21486511:A:C (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 rs777214281

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.post596+ae089ad