rs4455882
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021021.4(SNTB1):c.1136+4043T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 439,396 control chromosomes in the GnomAD database, including 74,923 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.46 ( 18596 hom., cov: 32)
Exomes 𝑓: 0.61 ( 56327 hom. )
Consequence
SNTB1
NM_021021.4 intron
NM_021021.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0750
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=-0.66).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNTB1 | NM_021021.4 | c.1136+4043T>C | intron_variant | ENST00000517992.2 | |||
SNTB1 | XM_047422126.1 | c.557+4043T>C | intron_variant | ||||
SNTB1 | XM_047422127.1 | c.557+4043T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNTB1 | ENST00000517992.2 | c.1136+4043T>C | intron_variant | 1 | NM_021021.4 | P1 | |||
SNTB1 | ENST00000519177.5 | n.1178T>C | non_coding_transcript_exon_variant | 5/5 | 1 | ||||
SNTB1 | ENST00000395601.7 | c.1136+4043T>C | intron_variant | 5 | P1 | ||||
SNTB1 | ENST00000648490.1 | c.1136+4043T>C | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.461 AC: 70070AN: 151954Hom.: 18591 Cov.: 32
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GnomAD4 exome AF: 0.614 AC: 176519AN: 287324Hom.: 56327 Cov.: 5 AF XY: 0.607 AC XY: 88133AN XY: 145152
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GnomAD4 genome AF: 0.461 AC: 70105AN: 152072Hom.: 18596 Cov.: 32 AF XY: 0.458 AC XY: 34047AN XY: 74322
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at