rs4619789

Variant names:

• chr3-97413080-G-C
• rs4619789
• NM_001080448.3:c.1731+7806G>C

Variant summary

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

The NM_001080448.3(EPHA6):​c.1731+7806G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 151,582 control chromosomes in the GnomAD database, including 5,321 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 0.15 (5321 hom., cov: 32)
• Consequence: EPHA6 NM_001080448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• 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]

ENSG00000296578 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 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.1731+7806G>C		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.1731+7806G>C		intron	N/A	ENSP00000374323.5	A0A0B4J1T8
	ENSG00000296578	ENST00000740547.1		n.329+972C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22565 AN: 151464 Hom.: 5287 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0839

Gnomad ASJ AF: 0.0263

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.00810

Gnomad FIN AF: 0.000855

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.00395

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.149 AC: 22653 AN: 151582 Hom.: 5321 Cov.: 32 AF XY: 0.144 AC XY: 10685 AN XY: 74076

African (AFR) AF: 0.500 AC: 20624 AN: 41280

American (AMR) AF: 0.0841 AC: 1276 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.0263 AC: 91 AN: 3462

East Asian (EAS) AF: 0.0138 AC: 71 AN: 5152

South Asian (SAS) AF: 0.00748 AC: 36 AN: 4810

European-Finnish (FIN) AF: 0.000855 AC: 9 AN: 10526

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.00393 AC: 267 AN: 67870

Other (OTH) AF: 0.124 AC: 260 AN: 2100

Alfa AF: 0.0885 Hom.: 386

Bravo AF: 0.172

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.66
PhyloP100		-0.30
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: rs4619789; hg19: chr3-97131924;