chr3-96840425-T-G

Variant names:

• chr3-96840425-T-G
• rs2318155
• NM_001080448.3:c.385+25417T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080448.3(EPHA6):​c.385+25417T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0316 in 152,236 control chromosomes in the GnomAD database, including 111 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 0.032 (111 hom., cov: 32)
• Consequence: EPHA6 NM_001080448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHA6	NM_001080448.3	c.385+25417T>G		intron_variant	Intron 1 of 17	ENST00000389672.10	NP_001073917.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHA6	ENST00000389672.10	c.385+25417T>G		intron_variant	Intron 1 of 17	1	NM_001080448.3	ENSP00000374323.5
EPHA6	ENST00000506569.1	c.217+25417T>G		intron_variant	Intron 1 of 3	1		ENSP00000425132.1
EPHA6	ENST00000470610.6	c.385+25417T>G		intron_variant	Intron 1 of 4	2		ENSP00000420598.2

Frequencies

GnomAD3 genomes AF: 0.0317 AC: 4815 AN: 152118 Hom.: 112 Cov.: 32

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0297

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.0695

Gnomad SAS AF: 0.0633

Gnomad FIN AF: 0.00866

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0377

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0316 AC: 4814 AN: 152236 Hom.: 111 Cov.: 32 AF XY: 0.0304 AC XY: 2259 AN XY: 74414

African (AFR) AF: 0.0193 AC: 803 AN: 41568

American (AMR) AF: 0.0297 AC: 453 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3468

East Asian (EAS) AF: 0.0696 AC: 360 AN: 5170

South Asian (SAS) AF: 0.0633 AC: 305 AN: 4818

European-Finnish (FIN) AF: 0.00866 AC: 92 AN: 10626

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0377 AC: 2562 AN: 67994

Other (OTH) AF: 0.0374 AC: 79 AN: 2114

Alfa AF: 0.0326 Hom.: 11

Bravo AF: 0.0318

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.62
PhyloP100		0.075
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs2318155; hg19: chr3-96559269;