rs193920856
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The ENST00000263208.5(HIRA):c.820G>T(p.Val274Leu) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000684 in 1,461,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. 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. V274M) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000263208.5 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HIRA | NM_003325.4 | c.820G>T | p.Val274Leu | missense_variant, splice_region_variant | 8/25 | ENST00000263208.5 | NP_003316.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HIRA | ENST00000263208.5 | c.820G>T | p.Val274Leu | missense_variant, splice_region_variant | 8/25 | 1 | NM_003325.4 | ENSP00000263208 | P1 | |
HIRA | ENST00000340170.8 | c.820G>T | p.Val274Leu | missense_variant, splice_region_variant | 8/21 | 1 | ENSP00000345350 | |||
C22orf39 | ENST00000509549.5 | c.*696G>T | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 9/24 | 2 | ENSP00000424903 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727216
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at