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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.

rs375111736

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:216432809 (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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000016 (4/251438, GnomAD_exome)
T=0.000029 (4/140262, GnomAD)
T=0.000008 (1/121350, ExAC) (+ 2 more)
A=0.00003 (1/35430, ALFA)
A=0.00008 (1/13006, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SMARCAL1 : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 51792 C=0.99996 A=0.00002, T=0.00002
European Sub 36678 C=0.99997 A=0.00003, T=0.00000
African Sub 7754 C=0.9999 A=0.0000, T=0.0001
African Others Sub 298 C=1.000 A=0.000, T=0.000
African American Sub 7456 C=0.9999 A=0.0000, T=0.0001
Asian Sub 112 C=1.000 A=0.000, T=0.000
East Asian Sub 86 C=1.00 A=0.00, T=0.00
Other Asian Sub 26 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 500 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 628 C=1.000 A=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, T=0.00
Other Sub 6022 C=1.0000 A=0.0000, T=0.0000


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 251438 C=0.999984 T=0.000016
gnomAD - Exomes European Sub 135370 C=0.999985 T=0.000015
gnomAD - Exomes Asian Sub 49008 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34592 C=0.99997 T=0.00003
gnomAD - Exomes African Sub 16250 C=0.99994 T=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10080 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6138 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140262 C=0.999971 T=0.000029
gnomAD - Genomes European Sub 75962 C=0.99999 T=0.00001
gnomAD - Genomes African Sub 42030 C=0.99993 T=0.00007
gnomAD - Genomes American Sub 13662 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=1.0000 T=0.0000
ExAC Global Study-wide 121350 C=0.999992 T=0.000008
ExAC Europe Sub 73312 C=1.00000 T=0.00000
ExAC Asian Sub 25158 C=1.00000 T=0.00000
ExAC American Sub 11576 C=1.00000 T=0.00000
ExAC African Sub 10396 C=0.99990 T=0.00010
ExAC Other Sub 908 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 35430 C=0.99997 A=0.00003, T=0.00000
Allele Frequency Aggregator European Sub 26588 C=0.99996 A=0.00004, T=0.00000
Allele Frequency Aggregator Other Sub 4588 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2916 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00, T=0.00
GO Exome Sequencing Project Global Study-wide 13006 C=0.99992 A=0.00008
GO Exome Sequencing Project European American Sub 8600 C=0.9999 A=0.0001
GO Exome Sequencing Project African American Sub 4406 C=1.0000 A=0.0000
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 2 NC_000002.12:g.216432809C>A
GRCh38.p14 chr 2 NC_000002.12:g.216432809C>T
GRCh37.p13 chr 2 NC_000002.11:g.217297532C>A
GRCh37.p13 chr 2 NC_000002.11:g.217297532C>T
SMARCAL1 RefSeqGene (LRG_108) NG_009771.1:g.25396C>A
SMARCAL1 RefSeqGene (LRG_108) NG_009771.1:g.25396C>T
Gene: SMARCAL1, SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SMARCAL1 transcript variant 2 NM_001127207.2:c.1426C>A R [CGG] > R [AGG] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_001120679.1:p.Arg476= R (Arg) > R (Arg) Synonymous Variant
SMARCAL1 transcript variant 2 NM_001127207.2:c.1426C>T R [CGG] > W [TGG] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_001120679.1:p.Arg476Trp R (Arg) > W (Trp) Missense Variant
SMARCAL1 transcript variant 1 NM_014140.4:c.1426C>A R [CGG] > R [AGG] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_054859.2:p.Arg476= R (Arg) > R (Arg) Synonymous Variant
SMARCAL1 transcript variant 1 NM_014140.4:c.1426C>T R [CGG] > W [TGG] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_054859.2:p.Arg476Trp R (Arg) > W (Trp) 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 C= A T
GRCh38.p14 chr 2 NC_000002.12:g.216432809= NC_000002.12:g.216432809C>A NC_000002.12:g.216432809C>T
GRCh37.p13 chr 2 NC_000002.11:g.217297532= NC_000002.11:g.217297532C>A NC_000002.11:g.217297532C>T
SMARCAL1 RefSeqGene (LRG_108) NG_009771.1:g.25396= NG_009771.1:g.25396C>A NG_009771.1:g.25396C>T
SMARCAL1 transcript variant 1 NM_014140.4:c.1426= NM_014140.4:c.1426C>A NM_014140.4:c.1426C>T
SMARCAL1 transcript variant 1 NM_014140.3:c.1426= NM_014140.3:c.1426C>A NM_014140.3:c.1426C>T
SMARCAL1 transcript variant 2 NM_001127207.2:c.1426= NM_001127207.2:c.1426C>A NM_001127207.2:c.1426C>T
SMARCAL1 transcript variant 2 NM_001127207.1:c.1426= NM_001127207.1:c.1426C>A NM_001127207.1:c.1426C>T
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_054859.2:p.Arg476= NP_054859.2:p.Arg476= NP_054859.2:p.Arg476Trp
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_001120679.1:p.Arg476= NP_001120679.1:p.Arg476= NP_001120679.1:p.Arg476Trp
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#.

12 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712484162 Apr 25, 2013 (138)
2 JMKIDD_LAB ss974445607 Aug 21, 2014 (142)
3 JMKIDD_LAB ss1067445030 Aug 21, 2014 (142)
4 EVA_EXAC ss1686722950 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2239134072 Dec 20, 2016 (150)
6 GNOMAD ss2733313209 Nov 08, 2017 (151)
7 GNOMAD ss2746874302 Nov 08, 2017 (151)
8 GNOMAD ss2786309748 Nov 08, 2017 (151)
9 EVA ss3823852750 Apr 25, 2020 (154)
10 TOPMED ss4544582336 Apr 26, 2021 (155)
11 TOPMED ss4544582337 Apr 26, 2021 (155)
12 EVA ss5336022642 Oct 12, 2022 (156)
13 ExAC NC_000002.11 - 217297532 Oct 11, 2018 (152)
14 gnomAD - Genomes NC_000002.12 - 216432809 Apr 26, 2021 (155)
15 gnomAD - Exomes NC_000002.11 - 217297532 Jul 13, 2019 (153)
16 GO Exome Sequencing Project NC_000002.11 - 217297532 Oct 11, 2018 (152)
17 TopMed

Submission ignored due to conflicting rows:
Row 348405215 (NC_000002.12:216432808:C:A 1/264690)
Row 348405216 (NC_000002.12:216432808:C:T 8/264690)

- Apr 26, 2021 (155)
18 TopMed

Submission ignored due to conflicting rows:
Row 348405215 (NC_000002.12:216432808:C:A 1/264690)
Row 348405216 (NC_000002.12:216432808:C:T 8/264690)

- Apr 26, 2021 (155)
19 ALFA NC_000002.12 - 216432809 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
311163, ss712484162, ss3823852750 NC_000002.11:217297531:C:A NC_000002.12:216432808:C:A (self)
8266880284, ss4544582336 NC_000002.12:216432808:C:A NC_000002.12:216432808:C:A (self)
6626766, 2379713, ss974445607, ss1067445030, ss1686722950, ss2733313209, ss2746874302, ss2786309748, ss5336022642 NC_000002.11:217297531:C:T NC_000002.12:216432808:C:T (self)
90873576, 8266880284, ss2239134072, ss4544582337 NC_000002.12:216432808:C:T NC_000002.12:216432808: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 rs375111736

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.post761+d5e8e07