rs7640007

Variant names:

• chr3-97071021-G-A
• rs7640007
• NM_001080448.3:c.1114+83028G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-97071021-G-A
• chr3-97071021-G-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.1114+83028G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,928 control chromosomes in the GnomAD database, including 2,652 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 0.14 (2652 hom., cov: 32)
• Consequence: EPHA6 NM_001080448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.331 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPHA6	NM_001080448.3	MANE Select	c.1114+83028G>A		intron	N/A	NP_001073917.2	A0A0B4J1T8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPHA6	ENST00000389672.10	TSL:1 MANE Select	c.1114+83028G>A		intron	N/A	ENSP00000374323.5	A0A0B4J1T8
	EPHA6	ENST00000470610.6	TSL:2	c.1114+83028G>A		intron	N/A	ENSP00000420598.2	E7EU71

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21384 AN: 151810 Hom.: 2638 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.141 AC: 21445 AN: 151928 Hom.: 2652 Cov.: 32 AF XY: 0.138 AC XY: 10213 AN XY: 74272

African (AFR) AF: 0.335 AC: 13881 AN: 41392

American (AMR) AF: 0.0865 AC: 1317 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 318 AN: 3472

East Asian (EAS) AF: 0.0462 AC: 238 AN: 5156

South Asian (SAS) AF: 0.0810 AC: 390 AN: 4814

European-Finnish (FIN) AF: 0.0529 AC: 560 AN: 10584

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0638 AC: 4338 AN: 67962

Other (OTH) AF: 0.146 AC: 309 AN: 2114

Alfa AF: 0.0818 Hom.: 1370

Bravo AF: 0.152

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.72
PhyloP100		-0.028
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: rs7640007; hg19: chr3-96789865;