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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.

rs549213726

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:94603441 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000012 (3/250626, GnomAD_exome)
G=0.000008 (1/118732, ExAC)
G=0.0002 (1/6404, 1000G_30x) (+ 1 more)
G=0.0002 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SGCE : Missense Variant
CASD1 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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 250626 A=0.999988 G=0.000012
gnomAD - Exomes European Sub 134918 A=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 48872 A=0.99998 G=0.00002
gnomAD - Exomes American Sub 34468 A=0.99994 G=0.00006
gnomAD - Exomes African Sub 16206 A=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10058 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6104 A=1.0000 G=0.0000
ExAC Global Study-wide 118732 A=0.999992 G=0.000008
ExAC Europe Sub 71770 A=1.00000 G=0.00000
ExAC Asian Sub 24662 A=0.99996 G=0.00004
ExAC American Sub 11308 A=1.00000 G=0.00000
ExAC African Sub 10100 A=1.00000 G=0.00000
ExAC Other Sub 892 A=1.000 G=0.000
1000Genomes_30x Global Study-wide 6404 A=0.9998 G=0.0002
1000Genomes_30x African Sub 1786 A=1.0000 G=0.0000
1000Genomes_30x Europe Sub 1266 A=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 A=0.9992 G=0.0008
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=1.000 G=0.000
1000Genomes Global Study-wide 5008 A=0.9998 G=0.0002
1000Genomes African Sub 1322 A=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=1.0000 G=0.0000
1000Genomes South Asian Sub 978 A=0.999 G=0.001
1000Genomes American Sub 694 A=1.000 G=0.000
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 7 NC_000007.14:g.94603441A>G
GRCh37.p13 chr 7 NC_000007.13:g.94232753A>G
SGCE RefSeqGene (LRG_206) NG_008893.3:g.58132T>C
Gene: CASD1, CAS1 domain containing 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CASD1 transcript variant 2 NM_001363426.1:c. N/A Genic Downstream Transcript Variant
CASD1 transcript variant 3 NM_001363427.1:c. N/A Genic Downstream Transcript Variant
CASD1 transcript variant 4 NM_001363428.1:c. N/A Genic Downstream Transcript Variant
CASD1 transcript variant 1 NM_022900.5:c. N/A Genic Downstream Transcript Variant
CASD1 transcript variant X1 XM_011516495.3:c.2128-278…

XM_011516495.3:c.2128-27875A>G

N/A Intron Variant
CASD1 transcript variant X4 XM_006716093.4:c. N/A Genic Downstream Transcript Variant
CASD1 transcript variant X2 XR_007060138.1:n. N/A Intron Variant
CASD1 transcript variant X3 XR_007060139.1:n. N/A Intron Variant
CASD1 transcript variant X5 XR_007060140.1:n. N/A Intron Variant
Gene: SGCE, sarcoglycan epsilon (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SGCE transcript variant 2 NM_003919.3:c.674T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 2 NP_003910.1:p.Met225Thr M (Met) > T (Thr) Missense Variant
SGCE transcript variant 4 NM_001301139.2:c.551T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 4 NP_001288068.1:p.Met184Thr M (Met) > T (Thr) Missense Variant
SGCE transcript variant 7 NM_001346717.2:c.674T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 7 NP_001333646.1:p.Met225Thr M (Met) > T (Thr) Missense Variant
SGCE transcript variant 5 NM_001346713.2:c.782T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 5 precursor NP_001333642.1:p.Met261Thr M (Met) > T (Thr) Missense Variant
SGCE transcript variant 9 NM_001346720.2:c.401T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 9 NP_001333649.1:p.Met134Thr M (Met) > T (Thr) Missense Variant
SGCE transcript variant 12 NM_001362809.2:c.551T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 12 NP_001349738.1:p.Met184Thr M (Met) > T (Thr) Missense Variant
SGCE transcript variant 8 NM_001346719.2:c.587T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 8 NP_001333648.1:p.Met196Thr M (Met) > T (Thr) Missense Variant
SGCE transcript variant 6 NM_001346715.2:c.782T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 6 precursor NP_001333644.1:p.Met261Thr M (Met) > T (Thr) Missense Variant
SGCE transcript variant 3 NM_001099400.2:c.674T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 3 NP_001092870.1:p.Met225Thr M (Met) > T (Thr) Missense Variant
SGCE transcript variant 1 NM_001099401.2:c.674T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 1 NP_001092871.1:p.Met225Thr M (Met) > T (Thr) Missense Variant
SGCE transcript variant 11 NM_001362808.2:c.401T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 11 NP_001349737.1:p.Met134Thr M (Met) > T (Thr) Missense Variant
SGCE transcript variant 10 NM_001362807.2:c.587T>C M [ATG] > T [ACG] Coding Sequence Variant
epsilon-sarcoglycan isoform 10 NP_001349736.1:p.Met196Thr M (Met) > T (Thr) 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 A= G
GRCh38.p14 chr 7 NC_000007.14:g.94603441= NC_000007.14:g.94603441A>G
GRCh37.p13 chr 7 NC_000007.13:g.94232753= NC_000007.13:g.94232753A>G
SGCE RefSeqGene (LRG_206) NG_008893.3:g.58132= NG_008893.3:g.58132T>C
SGCE transcript variant 2 NM_003919.3:c.674= NM_003919.3:c.674T>C
SGCE transcript variant 2 NM_003919.2:c.674= NM_003919.2:c.674T>C
SGCE transcript variant 8 NM_001346719.2:c.587= NM_001346719.2:c.587T>C
SGCE transcript variant 8 NM_001346719.1:c.587= NM_001346719.1:c.587T>C
SGCE transcript variant 10 NM_001362807.2:c.587= NM_001362807.2:c.587T>C
SGCE transcript variant 10 NM_001362807.1:c.587= NM_001362807.1:c.587T>C
SGCE transcript variant 5 NM_001346713.2:c.782= NM_001346713.2:c.782T>C
SGCE transcript variant 5 NM_001346713.1:c.782= NM_001346713.1:c.782T>C
SGCE transcript variant 6 NM_001346715.2:c.782= NM_001346715.2:c.782T>C
SGCE transcript variant 6 NM_001346715.1:c.782= NM_001346715.1:c.782T>C
SGCE transcript variant 1 NM_001099401.2:c.674= NM_001099401.2:c.674T>C
SGCE transcript variant 1 NM_001099401.1:c.674= NM_001099401.1:c.674T>C
SGCE transcript variant 9 NM_001346720.2:c.401= NM_001346720.2:c.401T>C
SGCE transcript variant 9 NM_001346720.1:c.401= NM_001346720.1:c.401T>C
SGCE transcript variant 11 NM_001362808.2:c.401= NM_001362808.2:c.401T>C
SGCE transcript variant 11 NM_001362808.1:c.401= NM_001362808.1:c.401T>C
SGCE transcript variant 3 NM_001099400.2:c.674= NM_001099400.2:c.674T>C
SGCE transcript variant 3 NM_001099400.1:c.674= NM_001099400.1:c.674T>C
SGCE transcript variant 7 NM_001346717.2:c.674= NM_001346717.2:c.674T>C
SGCE transcript variant 7 NM_001346717.1:c.674= NM_001346717.1:c.674T>C
SGCE transcript variant 4 NM_001301139.2:c.551= NM_001301139.2:c.551T>C
SGCE transcript variant 4 NM_001301139.1:c.551= NM_001301139.1:c.551T>C
SGCE transcript variant 12 NM_001362809.2:c.551= NM_001362809.2:c.551T>C
SGCE transcript variant 12 NM_001362809.1:c.551= NM_001362809.1:c.551T>C
epsilon-sarcoglycan isoform 2 NP_003910.1:p.Met225= NP_003910.1:p.Met225Thr
epsilon-sarcoglycan isoform 8 NP_001333648.1:p.Met196= NP_001333648.1:p.Met196Thr
epsilon-sarcoglycan isoform 10 NP_001349736.1:p.Met196= NP_001349736.1:p.Met196Thr
epsilon-sarcoglycan isoform 5 precursor NP_001333642.1:p.Met261= NP_001333642.1:p.Met261Thr
epsilon-sarcoglycan isoform 6 precursor NP_001333644.1:p.Met261= NP_001333644.1:p.Met261Thr
epsilon-sarcoglycan isoform 1 NP_001092871.1:p.Met225= NP_001092871.1:p.Met225Thr
epsilon-sarcoglycan isoform 9 NP_001333649.1:p.Met134= NP_001333649.1:p.Met134Thr
epsilon-sarcoglycan isoform 11 NP_001349737.1:p.Met134= NP_001349737.1:p.Met134Thr
epsilon-sarcoglycan isoform 3 NP_001092870.1:p.Met225= NP_001092870.1:p.Met225Thr
epsilon-sarcoglycan isoform 7 NP_001333646.1:p.Met225= NP_001333646.1:p.Met225Thr
epsilon-sarcoglycan isoform 4 NP_001288068.1:p.Met184= NP_001288068.1:p.Met184Thr
epsilon-sarcoglycan isoform 12 NP_001349738.1:p.Met184= NP_001349738.1:p.Met184Thr
CASD1 transcript variant X1 XM_011516495.3:c.2128-27875= XM_011516495.3:c.2128-27875A>G
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 submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1326201498 Aug 21, 2014 (142)
2 EVA_EXAC ss1688822542 Apr 01, 2015 (144)
3 GNOMAD ss2736569472 Nov 08, 2017 (151)
4 EVA ss5375280762 Oct 13, 2022 (156)
5 1000G_HIGH_COVERAGE ss5562628677 Oct 13, 2022 (156)
6 EVA ss5859949512 Oct 13, 2022 (156)
7 1000Genomes NC_000007.13 - 94232753 Oct 12, 2018 (152)
8 1000Genomes_30x NC_000007.14 - 94603441 Oct 13, 2022 (156)
9 ExAC NC_000007.13 - 94232753 Oct 12, 2018 (152)
10 gnomAD - Exomes NC_000007.13 - 94232753 Jul 13, 2019 (153)
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
38210320, 8894900, 5732590, ss1326201498, ss1688822542, ss2736569472, ss5375280762 NC_000007.13:94232752:A:G NC_000007.14:94603440:A:G (self)
50154612, ss5562628677, ss5859949512 NC_000007.14:94603440:A:G NC_000007.14:94603440:A:G
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 rs549213726

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