Variant 6-93258133-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_004440.4(EPHA7):c.2076G>A(p.Pro692=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 1,612,476 control chromosomes in the GnomAD database, including 413,340 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.69 ( 36230 hom., cov: 30)

Exomes 𝑓: 0.72 ( 377110 hom. )

Consequence

EPHA7
NM_004440.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0240

Variant links:

Genes affected

EPHA7 (HGNC:3390): (EPH receptor A7) 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. Increased expression of this gene is associated with multiple forms of carcinoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

EPHA7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 6-93258133-C-T is Benign according to our data. Variant chr6-93258133-C-T is described in ClinVar as [Benign]. Clinvar id is 1331194.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.024 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHA7	NM_004440.4 linkuse as main transcript	c.2076G>A	p.Pro692=	synonymous_variant	11/17	ENST00000369303.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHA7	ENST00000369303.9 linkuse as main transcript	c.2076G>A	p.Pro692=	synonymous_variant	11/17	1	NM_004440.4	P3	Q15375-1

Frequencies

GnomAD3 genomes

AF:

0.688

AC:

104407

AN:

151704

Hom.:

36213

Cov.:

show subpopulations

Gnomad AFR

AF:

0.607

Gnomad AMI

AF:

0.632

Gnomad AMR

AF:

0.711

Gnomad ASJ

AF:

0.725

Gnomad EAS

AF:

0.809

Gnomad SAS

AF:

0.834

Gnomad FIN

AF:

0.722

Gnomad MID

AF:

0.782

Gnomad NFE

AF:

0.706

Gnomad OTH

AF:

0.699

GnomAD3 exomes

AF:

0.720

AC:

180801

AN:

250988

Hom.:

65584

AF XY:

0.728

AC XY:

98760

AN XY:

135674

show subpopulations

Gnomad AFR exome

AF:

0.599

Gnomad AMR exome

AF:

0.681

Gnomad ASJ exome

AF:

0.739

Gnomad EAS exome

AF:

0.803

Gnomad SAS exome

AF:

0.834

Gnomad FIN exome

AF:

0.705

Gnomad NFE exome

AF:

0.706

Gnomad OTH exome

AF:

0.727

GnomAD4 exome

AF:

0.717

AC:

1047550

AN:

1460652

Hom.:

377110

Cov.:

AF XY:

0.722

AC XY:

524276

AN XY:

726632

show subpopulations

Gnomad4 AFR exome

AF:

0.590

Gnomad4 AMR exome

AF:

0.685

Gnomad4 ASJ exome

AF:

0.742

Gnomad4 EAS exome

AF:

0.838

Gnomad4 SAS exome

AF:

0.837

Gnomad4 FIN exome

AF:

0.705

Gnomad4 NFE exome

AF:

0.708

Gnomad4 OTH exome

AF:

0.726

GnomAD4 genome

AF:

0.688

AC:

104465

AN:

151824

Hom.:

36230

Cov.:

AF XY:

0.697

AC XY:

51698

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.607

Gnomad4 AMR

AF:

0.711

Gnomad4 ASJ

AF:

0.725

Gnomad4 EAS

AF:

0.809

Gnomad4 SAS

AF:

0.834

Gnomad4 FIN

AF:

0.722

Gnomad4 NFE

AF:

0.706

Gnomad4 OTH

AF:

0.701

Alfa

AF:

0.700

Hom.:

21643

Bravo

AF:

0.678

Asia WGS

AF:

0.803

AC:

2791

AN:

3478

EpiCase

AF:

0.721

EpiControl

AF:

0.719

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 30, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

7.2

DANN

Benign

0.55

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over