chr7-130672770-G-A
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_052933.4(TSGA13):c.494C>T(p.Ser165Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_052933.4 missense
Scores
Clinical Significance
Conservation
Publications
Genome browser will be placed here
ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSGA13 | NM_052933.4 | c.494C>T | p.Ser165Leu | missense_variant | Exon 6 of 8 | ENST00000356588.8 | NP_443165.1 | |
TSGA13 | NM_001304968.2 | c.494C>T | p.Ser165Leu | missense_variant | Exon 7 of 9 | NP_001291897.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152168Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000716 AC: 18AN: 251314 AF XY: 0.0000736 show subpopulations
GnomAD4 exome AF: 0.0000595 AC: 87AN: 1461734Hom.: 0 Cov.: 31 AF XY: 0.0000633 AC XY: 46AN XY: 727166 show subpopulations
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74462 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:1
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