rs9272699
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_002122.5(HLA-DQA1):c.225C>A(p.Ser75Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0219 in 78,214 control chromosomes in the GnomAD database, including 107 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002122.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-DQA1 | NM_002122.5 | c.225C>A | p.Ser75Arg | missense_variant | 2/5 | ENST00000343139.11 | |
HLA-DQA1 | XM_006715079.5 | c.225C>A | p.Ser75Arg | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-DQA1 | ENST00000343139.11 | c.225C>A | p.Ser75Arg | missense_variant | 2/5 | NM_002122.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0219 AC: 1712AN: 78132Hom.: 107 Cov.: 13
GnomAD3 exomes AF: 0.130 AC: 21202AN: 163220Hom.: 6050 AF XY: 0.129 AC XY: 11555AN XY: 89410
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0108 AC: 9846AN: 915470Hom.: 3978 Cov.: 26 AF XY: 0.0126 AC XY: 5765AN XY: 458564
GnomAD4 genome ? AF: 0.0219 AC: 1710AN: 78214Hom.: 107 Cov.: 13 AF XY: 0.0207 AC XY: 787AN XY: 38044
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at