chr12-6453708-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_018009.5(TAPBPL):c.557G>A(p.Arg186Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000464 in 1,594,158 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018009.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAPBPL | NM_018009.5 | c.557G>A | p.Arg186Gln | missense_variant | 3/7 | ENST00000266556.8 | NP_060479.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAPBPL | ENST00000266556.8 | c.557G>A | p.Arg186Gln | missense_variant | 3/7 | 1 | NM_018009.5 | ENSP00000266556 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152134Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000336 AC: 8AN: 237946Hom.: 0 AF XY: 0.0000232 AC XY: 3AN XY: 129408
GnomAD4 exome AF: 0.0000437 AC: 63AN: 1442024Hom.: 1 Cov.: 47 AF XY: 0.0000433 AC XY: 31AN XY: 715354
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152134Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74332
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at