rs10090787
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021021.4(SNTB1):c.571+12964G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,792 control chromosomes in the GnomAD database, including 9,253 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (★).
Frequency
Genomes: 𝑓 0.34 ( 9253 hom., cov: 32)
Consequence
SNTB1
NM_021021.4 intron
NM_021021.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.32
Genes affected
SNTB1 (HGNC:11168): (syntrophin beta 1) Dystrophin is a large, rod-like cytoskeletal protein found at the inner surface of muscle fibers. Dystrophin is missing in Duchenne Muscular Dystrophy patients and is present in reduced amounts in Becker Muscular Dystrophy patients. The protein encoded by this gene is a peripheral membrane protein found associated with dystrophin and dystrophin-related proteins. This gene is a member of the syntrophin gene family, which contains at least two other structurally-related genes. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNTB1 | NM_021021.4 | c.571+12964G>A | intron_variant | ENST00000517992.2 | NP_066301.1 | |||
SNTB1 | XM_011517239.3 | c.571+12964G>A | intron_variant | XP_011515541.1 | ||||
SNTB1 | XM_047422126.1 | c.-9+4475G>A | intron_variant | XP_047278082.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNTB1 | ENST00000517992.2 | c.571+12964G>A | intron_variant | 1 | NM_021021.4 | ENSP00000431124.1 | ||||
SNTB1 | ENST00000519177.5 | n.291+12964G>A | intron_variant | 1 | ||||||
SNTB1 | ENST00000395601.7 | c.571+12964G>A | intron_variant | 5 | ENSP00000378965.3 | |||||
SNTB1 | ENST00000648490.1 | n.571+12964G>A | intron_variant | ENSP00000497707.1 |
Frequencies
GnomAD3 genomes AF: 0.340 AC: 51551AN: 151674Hom.: 9228 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.340 AC: 51629AN: 151792Hom.: 9253 Cov.: 32 AF XY: 0.340 AC XY: 25241AN XY: 74196
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ClinVar
Significance: association
Submissions summary: Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lip and oral cavity carcinoma Other:1
association, criteria provided, single submitter | case-control | Department of Biological Science, Sunandan Divatia School of Science, NMIMS University | Jan 01, 2016 | The homozygous WT (CC) genotype showed a higher frequency in cases as compared to controls and indicated decreased risk to oral cancer with an OR 0.774 (0.60-0.99). - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at