rs2710646

Positions:

• chr2-62907744-C-A

Variant summary

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

The NM_001142616.3(EHBP1):​c.1185+33212C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,200 control chromosomes in the GnomAD database, including 1,698 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 0.13 (1698 hom., cov: 32)
• Consequence: EHBP1 NM_001142616.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EHBP1	NM_001142616.3	c.1185+33212C>A		intron_variant		ENST00000431489.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EHBP1	ENST00000431489.6	c.1185+33212C>A		intron_variant		1	NM_001142616.3	A1
EHBP1	ENST00000263991.9	c.1290+33212C>A		intron_variant		1		P3
EHBP1	ENST00000405289.5	c.1185+33212C>A		intron_variant		1		A1
EHBP1	ENST00000405015.7	c.1185+33212C>A		intron_variant		2		A1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20247 AN: 152082 Hom.: 1697 Cov.: 32

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.133 AC: 20236 AN: 152200 Hom.: 1698 Cov.: 32 AF XY: 0.133 AC XY: 9877 AN XY: 74412

Gnomad4 AFR AF: 0.0368

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.0468

Gnomad4 SAS AF: 0.0993

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.158

Alfa AF: 0.173 Hom.: 4831

Bravo AF: 0.132

Asia WGS AF: 0.0810 AC: 282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.57

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: rs2710646; hg19: chr2-63134879;