2-62845073-A-G

Position:

• chr2-62845073-A-G

Variant summary

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

The NM_001142616.3(EHBP1):​c.634+13915A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,034 control chromosomes in the GnomAD database, including 57,113 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 0.86 (57113 hom., cov: 29)
• Consequence: EHBP1 NM_001142616.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

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]

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EHBP1	NM_001142616.3	c.634+13915A>G		intron_variant		ENST00000431489.6	NP_001136088.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EHBP1	ENST00000431489.6	c.634+13915A>G		intron_variant		1	NM_001142616.3	ENSP00000403783	A1
	ENST00000452397.1	n.66+13300T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130770 AN: 151918 Hom.: 57072 Cov.: 29

Gnomad AFR AF: 0.965

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.861 AC: 130869 AN: 152034 Hom.: 57113 Cov.: 29 AF XY: 0.856 AC XY: 63581 AN XY: 74296

Gnomad4 AFR AF: 0.965

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.943

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.865

Alfa AF: 0.848 Hom.: 75924

Bravo AF: 0.866

Asia WGS AF: 0.533 AC: 1858 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	1.8
DANN	Benign	0.68

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: rs1877026; hg19: chr2-63072208;