rs12405694

chr1-16144960-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004431.5(EPHA2):c.823+3418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,142 control chromosomes in the GnomAD database, including 7,304 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 0.30 (7304 hom., cov: 33)
• Consequence: EPHA2 NM_004431.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHA2	NM_004431.5	c.823+3418T>C		intron_variant		ENST00000358432.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHA2	ENST00000358432.8	c.823+3418T>C		intron_variant		1	NM_004431.5	P1
EPHA2	ENST00000480202.1	n.28+1463T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45503 AN: 152022 Hom.: 7297 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.0256

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.338

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.299 AC: 45524 AN: 152142 Hom.: 7304 Cov.: 33 AF XY: 0.298 AC XY: 22164 AN XY: 74402

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.0259

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.340

Alfa AF: 0.317 Hom.: 1303

Bravo AF: 0.298

Asia WGS AF: 0.196 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.062
Dann	Benign	0.70

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

Other links and lift over

dbSNP: rs12405694; hg19: chr1-16471455;