3-97609440-G-T

Variant names:

• chr3-97609440-G-T
• rs2317212
• NM_001080448.3:c.2513-1353G>T

Variant summary

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

The NM_001080448.3(EPHA6):​c.2513-1353G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,076 control chromosomes in the GnomAD database, including 10,977 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 (10977 hom., cov: 32)
• Consequence: EPHA6 NM_001080448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHA6	NM_001080448.3	c.2513-1353G>T		intron_variant	Intron 12 of 17	ENST00000389672.10	NP_001073917.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHA6	ENST00000389672.10	c.2513-1353G>T		intron_variant	Intron 12 of 17	1	NM_001080448.3	ENSP00000374323.5

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47722 AN: 150958 Hom.: 10939 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.0936

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.317 AC: 47817 AN: 151076 Hom.: 10977 Cov.: 32 AF XY: 0.317 AC XY: 23431 AN XY: 73842

African (AFR) AF: 0.609 AC: 25178 AN: 41338

American (AMR) AF: 0.401 AC: 6060 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.0936 AC: 323 AN: 3450

East Asian (EAS) AF: 0.514 AC: 2648 AN: 5148

South Asian (SAS) AF: 0.252 AC: 1210 AN: 4808

European-Finnish (FIN) AF: 0.153 AC: 1617 AN: 10576

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.151 AC: 10140 AN: 67342

Other (OTH) AF: 0.284 AC: 597 AN: 2100

Alfa AF: 0.225 Hom.: 11440

Bravo AF: 0.350

Asia WGS AF: 0.411 AC: 1425 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.24
DANN	Benign	0.42
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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: rs2317212; hg19: chr3-97328284;