3-97627774-G-A

Variant names:

• chr3-97627774-G-A
• rs301927
• NM_001080448.3:c.2575-10099G>A

Variant summary

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

The NM_001080448.3(EPHA6):​c.2575-10099G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,672 control chromosomes in the GnomAD database, including 38,844 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 0.68 (38844 hom., cov: 31)
• Consequence: EPHA6 NM_001080448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 13 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080448.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPHA6	NM_001080448.3	MANE Select	c.2575-10099G>A		intron	N/A	NP_001073917.2
	EPHA6	NM_001278300.2		c.751-10099G>A		intron	N/A	NP_001265229.1
	EPHA6	NM_173655.4		c.751-10099G>A		intron	N/A	NP_775926.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPHA6	ENST00000389672.10	TSL:1 MANE Select	c.2575-10099G>A		intron	N/A	ENSP00000374323.5
	EPHA6	ENST00000514100.5	TSL:1	c.751-10099G>A		intron	N/A	ENSP00000421711.1
	EPHA6	ENST00000502694.1	TSL:1	c.751-10099G>A		intron	N/A	ENSP00000423950.1

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103870 AN: 151556 Hom.: 38847 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.685 AC: 103876 AN: 151672 Hom.: 38844 Cov.: 31 AF XY: 0.684 AC XY: 50701 AN XY: 74110

African (AFR) AF: 0.410 AC: 16957 AN: 41360

American (AMR) AF: 0.609 AC: 9231 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3090 AN: 3464

East Asian (EAS) AF: 0.353 AC: 1807 AN: 5126

South Asian (SAS) AF: 0.744 AC: 3586 AN: 4820

European-Finnish (FIN) AF: 0.846 AC: 8946 AN: 10570

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57572 AN: 67850

Other (OTH) AF: 0.723 AC: 1526 AN: 2110

Alfa AF: 0.788 Hom.: 87590

Bravo AF: 0.653

Asia WGS AF: 0.530 AC: 1845 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.48
PhyloP100		-0.036
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: rs301927; hg19: chr3-97346618;