chr8-23043188-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003842.5(TNFRSF10B):c.200C>T(p.Ala67Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0757 in 1,613,848 control chromosomes in the GnomAD database, including 6,251 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003842.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFRSF10B | NM_003842.5 | c.200C>T | p.Ala67Val | missense_variant | 2/9 | ENST00000276431.9 | |
TNFRSF10B | NM_147187.3 | c.200C>T | p.Ala67Val | missense_variant | 2/10 | ||
TNFRSF10B | NR_027140.2 | n.282-12316C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFRSF10B | ENST00000276431.9 | c.200C>T | p.Ala67Val | missense_variant | 2/9 | 1 | NM_003842.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0694 AC: 10547AN: 152016Hom.: 612 Cov.: 32
GnomAD3 exomes AF: 0.0967 AC: 24279AN: 251018Hom.: 1923 AF XY: 0.0902 AC XY: 12245AN XY: 135680
GnomAD4 exome AF: 0.0764 AC: 111663AN: 1461714Hom.: 5641 Cov.: 31 AF XY: 0.0748 AC XY: 54399AN XY: 727154
GnomAD4 genome AF: 0.0693 AC: 10544AN: 152134Hom.: 610 Cov.: 32 AF XY: 0.0704 AC XY: 5237AN XY: 74366
ClinVar
Submissions by phenotype
TNFRSF10B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at