6-32853049-G-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_000593.6(TAP1):c.588C>G(p.Leu196=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,612,328 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L196L) has been classified as Likely benign.
Frequency
Consequence
NM_000593.6 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAP1 | NM_000593.6 | c.588C>G | p.Leu196= | synonymous_variant | 1/11 | ENST00000354258.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAP1 | ENST00000354258.5 | c.588C>G | p.Leu196= | synonymous_variant | 1/11 | 1 | NM_000593.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000565 AC: 86AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000210 AC: 51AN: 242616Hom.: 0 AF XY: 0.000158 AC XY: 21AN XY: 133262
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1459998Hom.: 0 Cov.: 32 AF XY: 0.0000468 AC XY: 34AN XY: 726372
GnomAD4 genome ? AF: 0.000571 AC: 87AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.000470 AC XY: 35AN XY: 74500
ClinVar
Submissions by phenotype
MHC class I deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 23, 2023 | - - |
TAP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 23, 2019 | This variant is classified as likely 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