rs17464981

Positions:

• chr1-37726865-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001099439.2(EPHA10):​c.1772+237A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0685 in 152,312 control chromosomes in the GnomAD database, including 459 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 0.069 (459 hom., cov: 33)
• Consequence: EPHA10 NM_001099439.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74

Genes affected

EPHA10 (HGNC:19987): (EPH receptor A10) Ephrin receptors, the largest subfamily of receptor tyrosine kinases (RTKs), and their ephrin ligands are important mediators of cell-cell communication regulating cell attachment, shape, and mobility in neuronal and epithelial cells (Aasheim et al., 2005 [PubMed 15777695]). See MIM 179610 for additional background on Eph receptors and ephrins.[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EPHA10	NM_001099439.2	c.1772+237A>G		intron_variant		ENST00000373048.9	NP_001092909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EPHA10	ENST00000373048.9	c.1772+237A>G		intron_variant		5	NM_001099439.2	ENSP00000362139	P1

Frequencies

GnomAD3 genomes AF: 0.0686 AC: 10441 AN: 152194 Hom.: 459 Cov.: 33

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0222

Gnomad SAS AF: 0.0347

Gnomad FIN AF: 0.0678

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0926

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

GnomAD4 genome AF: 0.0685 AC: 10438 AN: 152312 Hom.: 459 Cov.: 33 AF XY: 0.0660 AC XY: 4918 AN XY: 74480

Gnomad4 AFR AF: 0.0290

Gnomad4 AMR AF: 0.0729

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0221

Gnomad4 SAS AF: 0.0344

Gnomad4 FIN AF: 0.0678

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0841 Hom.: 309

Bravo AF: 0.0689

Asia WGS AF: 0.0210 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	18
DANN	Benign	0.83

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

Publications

LitVar

Other links and lift over

dbSNP: rs17464981; hg19: chr1-38192537; COSMIC: COSV57622371; COSMIC: COSV57622371;