rs2213260

Positions:

• chr3-97028084-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.1114+40091G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,966 control chromosomes in the GnomAD database, including 10,867 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 0.29 (10867 hom., cov: 32)
• Consequence: EPHA6 NM_001080448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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]

LOC107986103 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPHA6	NM_001080448.3	c.1114+40091G>A		intron_variant		ENST00000389672.10
LOC107986103	XR_001740810.2	n.4734G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPHA6	ENST00000389672.10	c.1114+40091G>A		intron_variant		1	NM_001080448.3	P1
EPHA6	ENST00000470610.6	c.1114+40091G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43282 AN: 151846 Hom.: 10820 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.0507

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0894

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.286 AC: 43394 AN: 151966 Hom.: 10867 Cov.: 32 AF XY: 0.284 AC XY: 21128 AN XY: 74280

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.0948

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0894

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.282

Alfa AF: 0.138 Hom.: 1557

Bravo AF: 0.325

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.67

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: rs2213260; hg19: chr3-96746928;