rs2230954
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002116.8(HLA-A):c.41C>A(p.Ser14Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000998 in 1,002,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002116.8 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-A | NM_002116.8 | c.41C>A | p.Ser14Ter | stop_gained | 1/8 | ENST00000376809.10 | |
LOC124901298 | XR_007059541.1 | n.813+2187G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-A | ENST00000376809.10 | c.41C>A | p.Ser14Ter | stop_gained | 1/8 | NM_002116.8 | P3 | ||
ENST00000429656.1 | n.474G>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 104268Hom.: 0 Cov.: 17 FAILED QC
GnomAD4 exome AF: 9.98e-7 AC: 1AN: 1002374Hom.: 0 Cov.: 30 AF XY: 0.00000200 AC XY: 1AN XY: 499664
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 104268Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0AN XY: 50196
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at