chr22-17739395-A-C
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The ENST00000342111.9(BID):āc.412T>Gā(p.Ter138GlyextTer69) variant causes a stop lost change. The variant allele was found at a frequency of 0.00000746 in 1,608,512 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 34)
Exomes š: 0.0000076 ( 0 hom. )
Consequence
BID
ENST00000342111.9 stop_lost
ENST00000342111.9 stop_lost
Scores
4
5
7
Clinical Significance
Conservation
PhyloP100: 5.11
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 Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Stoplost variant in ENST00000342111.9 Downstream stopcodon found after 133 codons.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BID | NM_001196.4 | c.317T>G | p.Val106Gly | missense_variant | 4/6 | ENST00000622694.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BID | ENST00000622694.5 | c.317T>G | p.Val106Gly | missense_variant | 4/6 | 1 | NM_001196.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000283 AC: 7AN: 246916Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134014
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GnomAD4 exome AF: 0.00000755 AC: 11AN: 1456296Hom.: 0 Cov.: 32 AF XY: 0.00000414 AC XY: 3AN XY: 724340
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74370
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.455T>G (p.V152G) alteration is located in exon 4 (coding exon 4) of the BID gene. This alteration results from a T to G substitution at nucleotide position 455, causing the valine (V) at amino acid position 152 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.;T;.;T;.;.;.;.
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;N
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;.;.;.;D;D;D;D;.
REVEL
Uncertain
Sift
Pathogenic
D;.;.;.;D;D;D;D;.
Sift4G
Uncertain
D;D;D;D;D;D;D;D;D
Polyphen
D;.;D;.;.;D;.;D;.
Vest4
MutPred
0.83
.;.;Gain of disorder (P = 0.0155);.;.;Gain of disorder (P = 0.0155);.;Gain of disorder (P = 0.0155);.;
MVP
MPC
ClinPred
D
GERP RS
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gMVP
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