chr5-157052513-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001173393.3(HAVCR1):c.521C>T(p.Thr174Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00196 in 1,601,450 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T174K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001173393.3 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 |
---|---|---|---|---|---|---|---|
HAVCR1 | NM_001173393.3 | c.521C>T | p.Thr174Met | missense_variant | 4/9 | ENST00000523175.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAVCR1 | ENST00000523175.6 | c.521C>T | p.Thr174Met | missense_variant | 4/9 | 1 | NM_001173393.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0105 AC: 1600AN: 151858Hom.: 34 Cov.: 35
GnomAD3 exomes AF: 0.00269 AC: 671AN: 249610Hom.: 12 AF XY: 0.00210 AC XY: 285AN XY: 135412
GnomAD4 exome AF: 0.00107 AC: 1546AN: 1449472Hom.: 27 Cov.: 63 AF XY: 0.000928 AC XY: 669AN XY: 720882
GnomAD4 genome AF: 0.0105 AC: 1600AN: 151978Hom.: 34 Cov.: 35 AF XY: 0.00985 AC XY: 732AN XY: 74322
ClinVar
Submissions by phenotype
HAVCR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 11, 2019 | 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