rs61731097
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004431.5(EPHA2):c.1621G>A(p.Val541Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00134 in 1,614,116 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004431.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHA2 | NM_004431.5 | c.1621G>A | p.Val541Met | missense_variant | 8/17 | ENST00000358432.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHA2 | ENST00000358432.8 | c.1621G>A | p.Val541Met | missense_variant | 8/17 | 1 | NM_004431.5 | P1 | |
EPHA2 | ENST00000480202.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00720 AC: 1095AN: 152146Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00182 AC: 457AN: 250962Hom.: 6 AF XY: 0.00128 AC XY: 174AN XY: 135758
GnomAD4 exome AF: 0.000726 AC: 1062AN: 1461852Hom.: 14 Cov.: 32 AF XY: 0.000600 AC XY: 436AN XY: 727226
GnomAD4 genome ? AF: 0.00720 AC: 1096AN: 152264Hom.: 8 Cov.: 32 AF XY: 0.00685 AC XY: 510AN XY: 74448
ClinVar
Submissions by phenotype
Cataract 6 multiple types Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 22, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at