22-19353365-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS2
The NM_003325.4(HIRA):c.2839G>A(p.Val947Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000775 in 1,612,630 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V947L) has been classified as Uncertain significance.
Frequency
Consequence
NM_003325.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIRA | NM_003325.4 | c.2839G>A | p.Val947Ile | missense_variant | 23/25 | ENST00000263208.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIRA | ENST00000263208.5 | c.2839G>A | p.Val947Ile | missense_variant | 23/25 | 1 | NM_003325.4 | P1 | |
HIRA | ENST00000340170.8 | c.2218G>A | p.Val740Ile | missense_variant | 19/21 | 1 | |||
C22orf39 | ENST00000509549.5 | c.*2609G>A | 3_prime_UTR_variant, NMD_transcript_variant | 23/24 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000407 AC: 102AN: 250818Hom.: 1 AF XY: 0.000332 AC XY: 45AN XY: 135694
GnomAD4 exome AF: 0.0000815 AC: 119AN: 1460464Hom.: 1 Cov.: 32 AF XY: 0.0000661 AC XY: 48AN XY: 726546
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74338
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 14, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at