rs2308911
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001242525.2(HLA-DPA1):āc.184A>Cā(p.Met62Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,579,094 control chromosomes in the GnomAD database, including 45,154 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M62K) has been classified as Likely benign.
Frequency
Consequence
NM_001242525.2 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-DPA1 | NM_033554.4 | c.184A>C | p.Met62Leu | missense_variant | 2/5 | ENST00000692443.1 | |
HLA-DPA1 | NM_001242525.2 | c.184A>C | p.Met62Leu | missense_variant | 3/6 | ||
HLA-DPA1 | NM_001242524.2 | c.184A>C | p.Met62Leu | missense_variant | 3/6 | ||
HLA-DPA1 | NM_001405020.1 | c.184A>C | p.Met62Leu | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-DPA1 | ENST00000692443.1 | c.184A>C | p.Met62Leu | missense_variant | 2/5 | NM_033554.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.285 AC: 43197AN: 151830Hom.: 8052 Cov.: 32
GnomAD3 exomes AF: 0.232 AC: 55816AN: 240502Hom.: 9863 AF XY: 0.230 AC XY: 30143AN XY: 130920
GnomAD4 exome AF: 0.196 AC: 279366AN: 1427146Hom.: 37086 Cov.: 33 AF XY: 0.199 AC XY: 141150AN XY: 711022
GnomAD4 genome ? AF: 0.285 AC: 43242AN: 151948Hom.: 8068 Cov.: 32 AF XY: 0.282 AC XY: 20953AN XY: 74284
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at