rs6669624
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004431.5(EPHA2):c.1738+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.086 in 1,541,078 control chromosomes in the GnomAD database, including 13,376 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.19 ( 5783 hom., cov: 33)
Exomes 𝑓: 0.074 ( 7593 hom. )
Consequence
EPHA2
NM_004431.5 intron
NM_004431.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.44
Genes affected
EPHA2 (HGNC:3386): (EPH receptor A2) This gene belongs to the ephrin receptor subfamily of the protein-tyrosine kinase family. EPH and EPH-related receptors have been implicated in mediating developmental events, particularly in the nervous system. Receptors in the EPH subfamily typically have a single kinase domain and an extracellular region containing a Cys-rich domain and 2 fibronectin type III repeats. The ephrin receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. This gene encodes a protein that binds ephrin-A ligands. Mutations in this gene are the cause of certain genetically-related cataract disorders.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
?
Variant 1-16133844-G-A is Benign according to our data. Variant chr1-16133844-G-A is described in ClinVar as [Benign]. Clinvar id is 259388.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHA2 | NM_004431.5 | c.1738+16C>T | intron_variant | ENST00000358432.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHA2 | ENST00000358432.8 | c.1738+16C>T | intron_variant | 1 | NM_004431.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.193 AC: 29399AN: 152044Hom.: 5766 Cov.: 33
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GnomAD3 exomes AF: 0.106 AC: 15965AN: 149950Hom.: 1706 AF XY: 0.0981 AC XY: 7701AN XY: 78476
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GnomAD4 exome AF: 0.0743 AC: 103140AN: 1388916Hom.: 7593 Cov.: 33 AF XY: 0.0739 AC XY: 50505AN XY: 683644
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GnomAD4 genome ? AF: 0.194 AC: 29458AN: 152162Hom.: 5783 Cov.: 33 AF XY: 0.193 AC XY: 14369AN XY: 74396
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Cataract 6 multiple types Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 29, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at