rs4404602

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000613740.5(EPHA5):​c.247-2791A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,020 control chromosomes in the GnomAD database, including 5,251 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.24 ( 5251 hom., cov: 31)

Consequence

EPHA5
ENST00000613740.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.446
Variant links:
Genes affected
EPHA5 (HGNC:3389): (EPH receptor A5) 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. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Aug 2013]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EPHA5NM_001281766.3 linkuse as main transcriptc.247-2791A>G intron_variant ENST00000613740.5 NP_001268695.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EPHA5ENST00000613740.5 linkuse as main transcriptc.247-2791A>G intron_variant 1 NM_001281766.3 ENSP00000478537 A2

Frequencies

GnomAD3 genomes
AF:
0.245
AC:
37174
AN:
151902
Hom.:
5232
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.142
Gnomad AMI
AF:
0.118
Gnomad AMR
AF:
0.379
Gnomad ASJ
AF:
0.340
Gnomad EAS
AF:
0.561
Gnomad SAS
AF:
0.276
Gnomad FIN
AF:
0.272
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.243
Gnomad OTH
AF:
0.270
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.245
AC:
37210
AN:
152020
Hom.:
5251
Cov.:
31
AF XY:
0.251
AC XY:
18623
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.142
Gnomad4 AMR
AF:
0.379
Gnomad4 ASJ
AF:
0.340
Gnomad4 EAS
AF:
0.562
Gnomad4 SAS
AF:
0.278
Gnomad4 FIN
AF:
0.272
Gnomad4 NFE
AF:
0.243
Gnomad4 OTH
AF:
0.275
Alfa
AF:
0.243
Hom.:
4155
Bravo
AF:
0.254
Asia WGS
AF:
0.439
AC:
1527
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.56
DANN
Benign
0.35

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: rs4404602; hg19: chr4-66470813; API