rs11538
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001196.4(BID):āc.528T>Cā(p.Asn176=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,614,094 control chromosomes in the GnomAD database, including 20,716 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: š 0.12 ( 1523 hom., cov: 33)
Exomes š: 0.15 ( 19193 hom. )
Consequence
BID
NM_001196.4 synonymous
NM_001196.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.506
Genes affected
BID (HGNC:1050): (BH3 interacting domain death agonist) This gene encodes a death agonist that heterodimerizes with either agonist BAX or antagonist BCL2, and thus regulate apoptosis. The encoded protein is a member of the BCL-2 family of cell death regulators. It is a mediator of mitochondrial damage induced by caspase-8 (CASP8); CASP8 cleaves this encoded protein, and the COOH-terminal part translocates to mitochondria where it triggers cytochrome c release. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Aug 2020]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP7
?
Synonymous conserved (PhyloP=0.506 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BID | NM_001196.4 | c.528T>C | p.Asn176= | synonymous_variant | 5/6 | ENST00000622694.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BID | ENST00000622694.5 | c.528T>C | p.Asn176= | synonymous_variant | 5/6 | 1 | NM_001196.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.123 AC: 18769AN: 152128Hom.: 1523 Cov.: 33
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GnomAD3 exomes AF: 0.128 AC: 32218AN: 251474Hom.: 2545 AF XY: 0.127 AC XY: 17202AN XY: 135908
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GnomAD4 exome AF: 0.155 AC: 225983AN: 1461848Hom.: 19193 Cov.: 33 AF XY: 0.152 AC XY: 110446AN XY: 727214
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GnomAD4 genome ? AF: 0.123 AC: 18774AN: 152246Hom.: 1523 Cov.: 33 AF XY: 0.122 AC XY: 9045AN XY: 74442
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at