rs41544112
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002123.5(HLA-DQB1):c.485G>A(p.Arg162Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0467 in 1,455,450 control chromosomes in the GnomAD database, including 7,618 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_002123.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HLA-DQB1 | ENST00000434651.7 | c.485G>A | p.Arg162Gln | missense_variant | Exon 3 of 5 | 6 | NM_002123.5 | ENSP00000407332.2 | ||
HLA-DQB1 | ENST00000374943.8 | c.485G>A | p.Arg162Gln | missense_variant | Exon 3 of 6 | 6 | ENSP00000364080.4 |
Frequencies
GnomAD3 genomes AF: 0.0558 AC: 6777AN: 121520Hom.: 505 Cov.: 18
GnomAD3 exomes AF: 0.0409 AC: 10011AN: 244568Hom.: 358 AF XY: 0.0411 AC XY: 5466AN XY: 133110
GnomAD4 exome AF: 0.0459 AC: 61243AN: 1333826Hom.: 7112 Cov.: 36 AF XY: 0.0451 AC XY: 30111AN XY: 668254
GnomAD4 genome AF: 0.0558 AC: 6788AN: 121624Hom.: 506 Cov.: 18 AF XY: 0.0545 AC XY: 3214AN XY: 58968
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at