rs2710642

chr2-62922422-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142616.3(EHBP1):c.1186-20296G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,036 control chromosomes in the GnomAD database, including 39,346 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 0.71 (39346 hom., cov: 31)
• Consequence: EHBP1 NM_001142616.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

Genes affected

EHBP1 (HGNC:29144): (EH domain binding protein 1) This gene encodes an Eps15 homology domain binding protein. The encoded protein may play a role in endocytic trafficking. A single nucleotide polymorphism in this gene is associated with an aggressive form of prostate cancer. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EHBP1	NM_001142616.3	c.1186-20296G>A		intron_variant		ENST00000431489.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EHBP1	ENST00000431489.6	c.1186-20296G>A		intron_variant		1	NM_001142616.3	A1
EHBP1	ENST00000263991.9	c.1291-20296G>A		intron_variant		1		P3
EHBP1	ENST00000405289.5	c.1186-20296G>A		intron_variant		1		A1
EHBP1	ENST00000405015.7	c.1186-20296G>A		intron_variant		2		A1

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108236 AN: 151916 Hom.: 39300 Cov.: 31

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.713 AC: 108346 AN: 152036 Hom.: 39346 Cov.: 31 AF XY: 0.707 AC XY: 52565 AN XY: 74304

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.675

Alfa AF: 0.675 Hom.: 20719

Bravo AF: 0.722

Asia WGS AF: 0.768 AC: 2673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	1.8
Dann	Benign	0.89

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: rs2710642; hg19: chr2-63149557;