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

Genomes: 𝑓 0.012 ( 28 hom., cov: 33)
Exomes 𝑓: 0.012 ( 130 hom. )

Consequence

EPHA2
ENST00000358432.8 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -5.87
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 1-16133292-C-A is Benign according to our data. Variant chr1-16133292-C-A is described in ClinVar as [Benign]. Clinvar id is 293418.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-16133292-C-A is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-5.87 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0115 (1756/152216) while in subpopulation AMR AF= 0.0233 (357/15302). AF 95% confidence interval is 0.0213. There are 28 homozygotes in gnomad4. There are 909 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1756 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EPHA2NM_004431.5 linkuse as main transcriptc.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
EPHA2ENST00000358432.8 linkuse as main transcriptc.1941G>T p.Thr647= synonymous_variant 11/171 NM_004431.5 ENSP00000351209 P1P29317-1
EPHA2ENST00000462805.1 linkuse as main transcriptn.159G>T non_coding_transcript_exon_variant 2/23

Frequencies

GnomAD3 genomes
AF:
0.0116
AC:
1757
AN:
152098
Hom.:
28
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00239
Gnomad AMI
AF:
0.00768
Gnomad AMR
AF:
0.0234
Gnomad ASJ
AF:
0.00979
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.0218
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.0142
Gnomad OTH
AF:
0.0229
GnomAD3 exomes
AF:
0.0111
AC:
2793
AN:
251252
Hom.:
18
AF XY:
0.0113
AC XY:
1539
AN XY:
135796
show subpopulations
Gnomad AFR exome
AF:
0.00246
Gnomad AMR exome
AF:
0.0114
Gnomad ASJ exome
AF:
0.00944
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00167
Gnomad FIN exome
AF:
0.0211
Gnomad NFE exome
AF:
0.0146
Gnomad OTH exome
AF:
0.0166
GnomAD4 exome
AF:
0.0124
AC:
18086
AN:
1461638
Hom.:
130
Cov.:
33
AF XY:
0.0123
AC XY:
8947
AN XY:
727124
show subpopulations
Gnomad4 AFR exome
AF:
0.00176
Gnomad4 AMR exome
AF:
0.0117
Gnomad4 ASJ exome
AF:
0.00930
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00153
Gnomad4 FIN exome
AF:
0.0202
Gnomad4 NFE exome
AF:
0.0137
Gnomad4 OTH exome
AF:
0.0123
GnomAD4 genome
AF:
0.0115
AC:
1756
AN:
152216
Hom.:
28
Cov.:
33
AF XY:
0.0122
AC XY:
909
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.00236
Gnomad4 AMR
AF:
0.0233
Gnomad4 ASJ
AF:
0.00979
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00145
Gnomad4 FIN
AF:
0.0218
Gnomad4 NFE
AF:
0.0142
Gnomad4 OTH
AF:
0.0227
Alfa
AF:
0.0102
Hom.:
3
Bravo
AF:
0.0117
Asia WGS
AF:
0.00202
AC:
8
AN:
3478
EpiCase
AF:
0.0161
EpiControl
AF:
0.0160

ClinVar

Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2024EPHA2: BP4, BP7, BS1, BS2 -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxOct 12, 2018- -
Cataract 6 multiple types Benign:2
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This 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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 11, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
CADD
Benign
0.34
DANN
Benign
0.77

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs56043737; hg19: chr1-16459787; API