chr22-19353405-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_003325.4(HIRA):c.2799C>T(p.His933His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00202 in 1,613,102 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003325.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HIRA | ENST00000263208.5 | c.2799C>T | p.His933His | synonymous_variant | Exon 23 of 25 | 1 | NM_003325.4 | ENSP00000263208.5 | ||
HIRA | ENST00000340170.8 | c.2178C>T | p.His726His | synonymous_variant | Exon 19 of 21 | 1 | ENSP00000345350.4 | |||
C22orf39 | ENST00000509549.5 | n.*2569C>T | non_coding_transcript_exon_variant | Exon 23 of 24 | 2 | ENSP00000424903.1 | ||||
C22orf39 | ENST00000509549.5 | n.*2569C>T | 3_prime_UTR_variant | Exon 23 of 24 | 2 | ENSP00000424903.1 |
Frequencies
GnomAD3 genomes AF: 0.00781 AC: 1189AN: 152188Hom.: 14 Cov.: 32
GnomAD3 exomes AF: 0.00319 AC: 799AN: 250166Hom.: 14 AF XY: 0.00244 AC XY: 331AN XY: 135428
GnomAD4 exome AF: 0.00142 AC: 2073AN: 1460796Hom.: 20 Cov.: 32 AF XY: 0.00126 AC XY: 916AN XY: 726692
GnomAD4 genome AF: 0.00781 AC: 1189AN: 152306Hom.: 14 Cov.: 32 AF XY: 0.00771 AC XY: 574AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:2
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HIRA-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at