rs719278

Positions:

• chr3-97685768-G-A

Variant summary

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

The NM_001080448.3(EPHA6):​c.2785-34493G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,032 control chromosomes in the GnomAD database, including 8,737 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 0.32 (8737 hom., cov: 32)
• Consequence: EPHA6 NM_001080448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441

Genes affected

EPHA6 (HGNC:19296): (EPH receptor A6) Predicted to enable transmembrane-ephrin receptor activity. Predicted to be involved in axon guidance; positive regulation of kinase activity; and transmembrane receptor protein tyrosine kinase signaling pathway. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

EPHA6 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPHA6	NM_001080448.3	c.2785-34493G>A		intron_variant		ENST00000389672.10	NP_001073917.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPHA6	ENST00000389672.10	c.2785-34493G>A		intron_variant		1	NM_001080448.3	ENSP00000374323.5
EPHA6	ENST00000477384.6	n.757-34493G>A		intron_variant		1		ENSP00000419470.2

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49387 AN: 151914 Hom.: 8740 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.325 AC: 49386 AN: 152032 Hom.: 8737 Cov.: 32 AF XY: 0.321 AC XY: 23839 AN XY: 74288

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.332

Alfa AF: 0.395 Hom.: 16339

Bravo AF: 0.324

Asia WGS AF: 0.282 AC: 984 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	1.9
DANN	Benign	0.62

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: rs719278; hg19: chr3-97404612;