chr2-217809974-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001387777.1(TNS1):c.5122G>A(p.Val1708Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 1,613,192 control chromosomes in the GnomAD database, including 293,610 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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_001387777.1 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 |
---|---|---|---|---|---|---|---|
TNS1 | NM_001387777.1 | c.5122G>A | p.Val1708Ile | missense_variant | 30/33 | ENST00000682258.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNS1 | ENST00000682258.1 | c.5122G>A | p.Val1708Ile | missense_variant | 30/33 | NM_001387777.1 | P2 |
Frequencies
GnomAD3 genomes AF: 0.643 AC: 97663AN: 151844Hom.: 32073 Cov.: 32
GnomAD3 exomes AF: 0.595 AC: 149216AN: 250916Hom.: 45044 AF XY: 0.586 AC XY: 79483AN XY: 135612
GnomAD4 exome AF: 0.596 AC: 870372AN: 1461230Hom.: 261486 Cov.: 56 AF XY: 0.592 AC XY: 430324AN XY: 726852
GnomAD4 genome AF: 0.643 AC: 97773AN: 151962Hom.: 32124 Cov.: 32 AF XY: 0.638 AC XY: 47414AN XY: 74278
ClinVar
Submissions by phenotype
TNS1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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