rs56043737
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The ENST00000358432.8(EPHA2):c.1941G>T(p.Thr647=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0123 in 1,613,854 control chromosomes in the GnomAD database, including 158 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T647T) has been classified as Likely benign.
Frequency
Consequence
ENST00000358432.8 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EPHA2 | NM_004431.5 | c.1941G>T | p.Thr647= | synonymous_variant | 11/17 | ENST00000358432.8 | NP_004422.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPHA2 | ENST00000358432.8 | c.1941G>T | p.Thr647= | synonymous_variant | 11/17 | 1 | NM_004431.5 | ENSP00000351209 | P1 | |
EPHA2 | ENST00000462805.1 | n.159G>T | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0116 AC: 1757AN: 152098Hom.: 28 Cov.: 33
GnomAD3 exomes AF: 0.0111 AC: 2793AN: 251252Hom.: 18 AF XY: 0.0113 AC XY: 1539AN XY: 135796
GnomAD4 exome AF: 0.0124 AC: 18086AN: 1461638Hom.: 130 Cov.: 33 AF XY: 0.0123 AC XY: 8947AN XY: 727124
GnomAD4 genome AF: 0.0115 AC: 1756AN: 152216Hom.: 28 Cov.: 33 AF XY: 0.0122 AC XY: 909AN XY: 74414
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | EPHA2: BP4, BP7, BS1, BS2 - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 12, 2018 | - - |
Cataract 6 multiple types Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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 | Labcorp Genetics (formerly Invitae), Labcorp | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at