2-62794915-T-C

Position:

• chr2-62794915-T-C

Variant summary

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

The NM_001142616.3(EHBP1):​c.312+23523T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 151,804 control chromosomes in the GnomAD database, including 29,305 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 0.62 (29305 hom., cov: 32)
• Consequence: EHBP1 NM_001142616.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

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=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EHBP1	NM_001142616.3	c.312+23523T>C		intron_variant		ENST00000431489.6	NP_001136088.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EHBP1	ENST00000431489.6	c.312+23523T>C		intron_variant		1	NM_001142616.3	ENSP00000403783	A1

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93618 AN: 151686 Hom.: 29266 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.806

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.617 AC: 93714 AN: 151804 Hom.: 29305 Cov.: 32 AF XY: 0.616 AC XY: 45698 AN XY: 74184

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.641

Alfa AF: 0.620 Hom.: 12887

Bravo AF: 0.618

Asia WGS AF: 0.420 AC: 1462 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	5.3
DANN	Benign	0.79

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: rs7591708; hg19: chr2-63022050;