3-97629466-A-G

Variant names:

• chr3-97629466-A-G
• rs301930
• NM_001080448.3:c.2575-8407A>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.2575-8407A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 152,012 control chromosomes in the GnomAD database, including 70,747 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 0.96 (70747 hom., cov: 30)
• Consequence: EPHA6 NM_001080448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 0 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHA6	NM_001080448.3	c.2575-8407A>G		intron_variant	Intron 13 of 17	ENST00000389672.10	NP_001073917.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHA6	ENST00000389672.10	c.2575-8407A>G		intron_variant	Intron 13 of 17	1	NM_001080448.3	ENSP00000374323.5

Frequencies

GnomAD3 genomes AF: 0.961 AC: 146036 AN: 151894 Hom.: 70691 Cov.: 30

Gnomad AFR AF: 0.985

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.961 AC: 146147 AN: 152012 Hom.: 70747 Cov.: 30 AF XY: 0.957 AC XY: 71103 AN XY: 74300

African (AFR) AF: 0.985 AC: 40882 AN: 41510

American (AMR) AF: 0.922 AC: 14031 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3351 AN: 3466

East Asian (EAS) AF: 0.574 AC: 2942 AN: 5126

South Asian (SAS) AF: 0.866 AC: 4178 AN: 4824

European-Finnish (FIN) AF: 0.983 AC: 10424 AN: 10602

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67127 AN: 67942

Other (OTH) AF: 0.951 AC: 2009 AN: 2112

Alfa AF: 0.961 Hom.: 32716

Bravo AF: 0.955

Asia WGS AF: 0.743 AC: 2586 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.95
DANN	Benign	0.47
PhyloP100		-0.025
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: rs301930; hg19: chr3-97348310;