6-32641349-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_002122.5(HLA-DQA1):c.122T>A(p.Phe41Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F41S) has been classified as Benign.
Frequency
Consequence
NM_002122.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-DQA1 | NM_002122.5 | c.122T>A | p.Phe41Tyr | missense_variant | 2/5 | ENST00000343139.11 | |
HLA-DQA1 | XM_006715079.5 | c.122T>A | p.Phe41Tyr | missense_variant | 2/4 | ||
HLA-DQA1-AS1 | XR_007059544.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-DQA1 | ENST00000343139.11 | c.122T>A | p.Phe41Tyr | missense_variant | 2/5 | NM_002122.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 15
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1004178Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 510542
GnomAD4 genome Cov.: 15
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at