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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.

rs748106387

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr2:216415427 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00003 (7/244472, GnomAD)
T=0.00002 (2/125568, TOPMED)
T=0.00003 (4/121410, ExAC) (+ 1 more)
T=0.0000 (1/30978, GnomAD)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SMARCAL1 : Stop Gained
Publications
1 citation
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 2 NC_000002.12:g.216415427C>A
GRCh38.p12 chr 2 NC_000002.12:g.216415427C>T
GRCh37.p13 chr 2 NC_000002.11:g.217280150C>A
GRCh37.p13 chr 2 NC_000002.11:g.217280150C>T
SMARCAL1 RefSeqGene (LRG_108) NG_009771.1:g.8014C>A
SMARCAL1 RefSeqGene (LRG_108) NG_009771.1:g.8014C>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 1 NM_014140.3:c.723C>A C [TGC] > * [TGA] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_054859.2:p.Cys241Ter C (Cys) > * (Ter) Stop Gained
SMARCAL1 transcript variant 1 NM_014140.3:c.723C>T C [TGC] > C [TGT] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_054859.2:p.Cys241= C (Cys) > C (Cys) Synonymous Variant
SMARCAL1 transcript variant 2 NM_001127207.1:c.723C>A C [TGC] > * [TGA] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_001120679.1:p.Cys241Ter C (Cys) > * (Ter) Stop Gained
SMARCAL1 transcript variant 2 NM_001127207.1:c.723C>T C [TGC] > C [TGT] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_001120679.1:p.Cys241= C (Cys) > C (Cys) Synonymous Variant
SMARCAL1 transcript variant X3 XM_017004228.2:c. N/A 5 Prime UTR Variant
SMARCAL1 transcript variant X1 XM_005246631.2:c.723C>A C [TGC] > * [TGA] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1 XP_005246688.1:p.Cys241Ter C (Cys) > * (Ter) Stop Gained
SMARCAL1 transcript variant X1 XM_005246631.2:c.723C>T C [TGC] > C [TGT] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1 XP_005246688.1:p.Cys241= C (Cys) > C (Cys) Synonymous Variant
SMARCAL1 transcript variant X2 XM_005246632.2:c.723C>A C [TGC] > * [TGA] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1 XP_005246689.1:p.Cys241Ter C (Cys) > * (Ter) Stop Gained
SMARCAL1 transcript variant X2 XM_005246632.2:c.723C>T C [TGC] > C [TGT] Coding Sequence Variant
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1 XP_005246689.1:p.Cys241= C (Cys) > C (Cys) 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.

Allele: A (allele ID: 360834 )
ClinVar Accession Disease Names Clinical Significance
RCV000414912.1 Atrioventricular canal defect,Congenital microcephaly,Decreased body weight,Disproportionate short-trunk short stature,Focal segmental glomerulosclerosis,Microcephaly,Short stature,Small for gestational age,Steroid-resistant nephrotic syndrome Pathogenic
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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 244472 C=0.99997 T=0.00003
gnomAD - Exomes European Sub 132234 C=1.00000 T=0.00000
gnomAD - Exomes Asian Sub 48030 C=1.0000 T=0.0000
gnomAD - Exomes American Sub 33582 C=0.9999 T=0.0001
gnomAD - Exomes African Sub 15302 C=0.9998 T=0.0002
gnomAD - Exomes Ashkenazi Jewish Sub 9850 C=1.000 T=0.000
gnomAD - Exomes Other Sub 5474 C=1.000 T=0.000
TopMed Global Study-wide 125568 C=0.99998 T=0.00002
ExAC Global Study-wide 121410 C=0.99997 T=0.00003
ExAC Europe Sub 73352 C=1.0000 T=0.0000
ExAC Asian Sub 25166 C=1.0000 T=0.0000
ExAC American Sub 11578 C=0.9998 T=0.0002
ExAC African Sub 10406 C=0.9999 T=0.0001
ExAC Other Sub 908 C=1.00 T=0.00
gnomAD - Genomes Global Study-wide 30978 C=1.0000 T=0.0000
gnomAD - Genomes European Sub 18498 C=0.9999 T=0.0001
gnomAD - Genomes African Sub 8736 C=1.000 T=0.000
gnomAD - Genomes East Asian Sub 1622 C=1.000 T=0.000
gnomAD - Genomes Other Sub 982 C=1.00 T=0.00
gnomAD - Genomes American Sub 838 C=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=1.00 T=0.00
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 Note
GRCh38.p12 chr 2 NC_000002.12:g.21...

NC_000002.12:g.216415427C=

NC_000002.12:g.21...

NC_000002.12:g.216415427C>A

NC_000002.12:g.21...

NC_000002.12:g.216415427C>T

GRCh37.p13 chr 2 NC_000002.11:g.21...

NC_000002.11:g.217280150C=

NC_000002.11:g.21...

NC_000002.11:g.217280150C>A

NC_000002.11:g.21...

NC_000002.11:g.217280150C>T

SMARCAL1 RefSeqGene (LRG_108) NG_009771.1:g.8014C= NG_009771.1:g.801...

NG_009771.1:g.8014C>A

NG_009771.1:g.801...

NG_009771.1:g.8014C>T

SMARCAL1 transcript variant 1 NM_014140.3:c.723C= NM_014140.3:c.723C>A NM_014140.3:c.723C>T
SMARCAL1 transcript variant 2 NM_001127207.1:c....

NM_001127207.1:c.723C=

NM_001127207.1:c....

NM_001127207.1:c.723C>A

NM_001127207.1:c....

NM_001127207.1:c.723C>T

SMARCAL1 transcript variant X1 XM_005246631.2:c....

XM_005246631.2:c.723C=

XM_005246631.2:c....

XM_005246631.2:c.723C>A

XM_005246631.2:c....

XM_005246631.2:c.723C>T

SMARCAL1 transcript variant X1 XM_005246631.1:c....

XM_005246631.1:c.723C=

XM_005246631.1:c....

XM_005246631.1:c.723C>A

XM_005246631.1:c....

XM_005246631.1:c.723C>T

SMARCAL1 transcript variant X2 XM_005246632.2:c....

XM_005246632.2:c.723C=

XM_005246632.2:c....

XM_005246632.2:c.723C>A

XM_005246632.2:c....

XM_005246632.2:c.723C>T

SMARCAL1 transcript variant X2 XM_005246632.1:c....

XM_005246632.1:c.723C=

XM_005246632.1:c....

XM_005246632.1:c.723C>A

XM_005246632.1:c....

XM_005246632.1:c.723C>T

SMARCAL1 transcript variant X3 XM_017004228.2:c....

XM_017004228.2:c.-194C=

XM_017004228.2:c....

XM_017004228.2:c.-194C>A

XM_017004228.2:c....

XM_017004228.2:c.-194C>T

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_054859.2:p.Cys...

NP_054859.2:p.Cys241=

NP_054859.2:p.Cys...

NP_054859.2:p.Cys241Ter

NP_054859.2:p.Cys...

NP_054859.2:p.Cys241=

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 NP_001120679.1:p....

NP_001120679.1:p.Cys241=

NP_001120679.1:p....

NP_001120679.1:p.Cys241Ter

NP_001120679.1:p....

NP_001120679.1:p.Cys241=

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1 XP_005246688.1:p....

XP_005246688.1:p.Cys241=

XP_005246688.1:p....

XP_005246688.1:p.Cys241Ter

XP_005246688.1:p....

XP_005246688.1:p.Cys241=

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1 XP_005246689.1:p....

XP_005246689.1:p.Cys241=

XP_005246689.1:p....

XP_005246689.1:p.Cys241Ter

XP_005246689.1:p....

XP_005246689.1:p.Cys241=

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#.

6 SubSNP, 4 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1686722736 Apr 01, 2015 (144)
2 CLINVAR ss2137463720 Jan 19, 2017 (149)
3 GNOMAD ss2733312910 Nov 08, 2017 (151)
4 GNOMAD ss2746874210 Nov 08, 2017 (151)
5 GNOMAD ss2786308434 Nov 08, 2017 (151)
6 TOPMED ss3338351737 Nov 08, 2017 (151)
7 ExAC NC_000002.11 - 217280150 Oct 11, 2018 (152)
8 gnomAD - Genomes NC_000002.11 - 217280150 Oct 11, 2018 (152)
9 gnomAD - Exomes NC_000002.11 - 217280150 Oct 11, 2018 (152)
10 TopMed NC_000002.12 - 216415427 Oct 11, 2018 (152)
11 ClinVar RCV000414912.1 Oct 11, 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
RCV000414912.1, ss2137463720 NC_000002.12:216415426:C:A NC_000002.12:216415426:C:A (self)
6626530, 115798295, 1889813, ss1686722736, ss2733312910, ss2746874210, ss2786308434 NC_000002.11:217280149:C:T NC_000002.12:216415426:C:T (self)
217475659, ss3338351737 NC_000002.12:216415426:C:T NC_000002.12:216415426: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.

1 citation for rs748106387
PMID Title Author Year Journal
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine

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