chr15-43197334-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_001114134.2(EPB42):c.2044G>A(p.Val682Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000179 in 1,614,174 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001114134.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000677 AC: 103AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000191 AC: 48AN: 251488Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135918
GnomAD4 exome AF: 0.000127 AC: 186AN: 1461888Hom.: 1 Cov.: 30 AF XY: 0.000111 AC XY: 81AN XY: 727246
GnomAD4 genome AF: 0.000676 AC: 103AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.000604 AC XY: 45AN XY: 74444
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Mar 01, 2023 | BP4_strong - |
Hereditary spherocytosis type 5 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 24, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jul 17, 2024 | The EPB42 c.2134G>A; p.Val712Ile variant (rs149419129), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 2041913). This variant is found in the African/African-American population with an allele frequency of 0.25% (62/24966 alleles) in the Genome Aggregation Database (v2.1.1). Computational analyses predict that this variant is neutral (REVEL: 0.122). Due to limited information, the clinical significance of this variant is uncertain at this time. - |
EPB42-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 08, 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