5-157095359-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_032782.5(HAVCR2):c.623G>C(p.Gly208Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000204 in 1,614,062 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032782.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAVCR2 | NM_032782.5 | c.623G>C | p.Gly208Ala | missense_variant | 5/7 | ENST00000307851.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAVCR2 | ENST00000307851.9 | c.623G>C | p.Gly208Ala | missense_variant | 5/7 | 1 | NM_032782.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00104 AC: 158AN: 152060Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000263 AC: 66AN: 251342Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135834
GnomAD4 exome AF: 0.000117 AC: 171AN: 1461884Hom.: 2 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727244
GnomAD4 genome ? AF: 0.00104 AC: 158AN: 152178Hom.: 0 Cov.: 31 AF XY: 0.000954 AC XY: 71AN XY: 74428
ClinVar
Submissions by phenotype
HAVCR2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 30, 2023 | This variant is classified as likely 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