3-50318299-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003773.5(HYAL2):c.1252A>C(p.Ile418Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 1,613,504 control chromosomes in the GnomAD database, including 13,055 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003773.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HYAL2 | NM_003773.5 | c.1252A>C | p.Ile418Leu | missense_variant | 4/4 | ENST00000357750.9 | |
HYAL2 | NM_033158.5 | c.1252A>C | p.Ile418Leu | missense_variant | 5/5 | ||
HYAL2 | XM_005265524.3 | c.1252A>C | p.Ile418Leu | missense_variant | 5/5 | ||
HYAL2 | XM_005265525.3 | c.1252A>C | p.Ile418Leu | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HYAL2 | ENST00000357750.9 | c.1252A>C | p.Ile418Leu | missense_variant | 4/4 | 1 | NM_003773.5 | P1 | |
HYAL2 | ENST00000395139.7 | c.1252A>C | p.Ile418Leu | missense_variant | 4/4 | 1 | P1 | ||
HYAL2 | ENST00000447092.5 | c.1252A>C | p.Ile418Leu | missense_variant | 3/3 | 1 | P1 | ||
HYAL2 | ENST00000442581.1 | c.1252A>C | p.Ile418Leu | missense_variant | 5/5 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.104 AC: 15854AN: 152196Hom.: 2293 Cov.: 32
GnomAD3 exomes AF: 0.121 AC: 30469AN: 250792Hom.: 7048 AF XY: 0.0988 AC XY: 13414AN XY: 135746
GnomAD4 exome AF: 0.0369 AC: 53907AN: 1461190Hom.: 10760 Cov.: 31 AF XY: 0.0334 AC XY: 24282AN XY: 726914
GnomAD4 genome ? AF: 0.104 AC: 15882AN: 152314Hom.: 2295 Cov.: 32 AF XY: 0.111 AC XY: 8253AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at