chr6-29943000-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002116.8(HLA-A):c.317G>T(p.Arg106Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000189 in 1,058,500 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 no classification for the single variant (no stars).
Frequency
Consequence
NM_002116.8 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-A | NM_002116.8 | c.317G>T | p.Arg106Leu | missense_variant | 2/8 | ENST00000376809.10 | |
LOC124901298 | XR_007059541.1 | n.813+1781C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-A | ENST00000376809.10 | c.317G>T | p.Arg106Leu | missense_variant | 2/8 | NM_002116.8 | P3 | ||
ENST00000429656.1 | n.68C>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 44562Hom.: 0 Cov.: 2 FAILED QC
GnomAD4 exome AF: 0.00000189 AC: 2AN: 1058500Hom.: 0 Cov.: 21 AF XY: 0.00000190 AC XY: 1AN XY: 526730
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 44562Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0AN XY: 21830
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at