3-50319607-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_003773.5(HYAL2):c.883C>T(p.Arg295Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,356 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_003773.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HYAL2 | NM_003773.5 | c.883C>T | p.Arg295Ter | stop_gained | 2/4 | ENST00000357750.9 | |
HYAL2 | NM_033158.5 | c.883C>T | p.Arg295Ter | stop_gained | 3/5 | ||
HYAL2 | XM_005265524.3 | c.883C>T | p.Arg295Ter | stop_gained | 3/5 | ||
HYAL2 | XM_005265525.3 | c.883C>T | p.Arg295Ter | stop_gained | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HYAL2 | ENST00000357750.9 | c.883C>T | p.Arg295Ter | stop_gained | 2/4 | 1 | NM_003773.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249802Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135410
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461134Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726842
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
HYAL2 deficiency Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | New Leaf Center | Dec 09, 2021 | From Fasham et al. 2021: Truncating variant expected to undergo nonsense-mediated decay. At extremely low frequency in gnomAD databases. In trans with p.(Arg277Cys). A strong consensus supporting a clinical diagnosis with a specific phenotype. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at