6-32832787-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001290043.2(TAP2):āc.983C>Gā(p.Ala328Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000539 in 1,612,810 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. A328A) has been classified as Likely benign.
Frequency
Consequence
NM_001290043.2 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 |
---|---|---|---|---|---|---|---|
TAP2 | NM_001290043.2 | c.983C>G | p.Ala328Gly | missense_variant | 6/12 | ENST00000374897.4 | |
TAP2 | NM_018833.3 | c.983C>G | p.Ala328Gly | missense_variant | 6/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAP2 | ENST00000374897.4 | c.983C>G | p.Ala328Gly | missense_variant | 6/12 | 1 | NM_001290043.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000631 AC: 96AN: 152094Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00104 AC: 257AN: 246388Hom.: 3 AF XY: 0.00141 AC XY: 189AN XY: 134334
GnomAD4 exome AF: 0.000530 AC: 774AN: 1460598Hom.: 9 Cov.: 35 AF XY: 0.000717 AC XY: 521AN XY: 726634
GnomAD4 genome AF: 0.000631 AC: 96AN: 152212Hom.: 3 Cov.: 32 AF XY: 0.000726 AC XY: 54AN XY: 74428
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
MHC class I deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at