rs74770812
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001290043.2(TAP2):c.1826C>T(p.Ala609Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00202 in 1,614,102 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. A609A) 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.1826C>T | p.Ala609Val | missense_variant | 11/12 | ENST00000374897.4 | |
TAP2 | NM_018833.3 | c.1826C>T | p.Ala609Val | missense_variant | 11/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAP2 | ENST00000374897.4 | c.1826C>T | p.Ala609Val | missense_variant | 11/12 | 1 | NM_001290043.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00951 AC: 1447AN: 152168Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00276 AC: 694AN: 251316Hom.: 8 AF XY: 0.00213 AC XY: 289AN XY: 135824
GnomAD4 exome AF: 0.00124 AC: 1818AN: 1461816Hom.: 20 Cov.: 54 AF XY: 0.00113 AC XY: 821AN XY: 727204
GnomAD4 genome ? AF: 0.00951 AC: 1449AN: 152286Hom.: 13 Cov.: 32 AF XY: 0.00878 AC XY: 654AN XY: 74466
ClinVar
Submissions by phenotype
MHC class I deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at