2-62845073-A-G

Variant names:

• chr2-62845073-A-G
• rs1877026
• NM_001142616.3:c.634+13915A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ENSG00000226605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142616.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EHBP1	NM_001142616.3	MANE Select	c.634+13915A>G		intron	N/A	NP_001136088.1	Q8NDI1-3
	EHBP1	NM_001354212.1		c.635-13333A>G		intron	N/A	NP_001341141.1	Q8NDI1-1
	EHBP1	NM_001354213.1		c.635-13333A>G		intron	N/A	NP_001341142.1	Q8NDI1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EHBP1	ENST00000431489.6	TSL:1 MANE Select	c.634+13915A>G		intron	N/A	ENSP00000403783.1	Q8NDI1-3
	EHBP1	ENST00000263991.9	TSL:1	c.635-13333A>G		intron	N/A	ENSP00000263991.5	Q8NDI1-1
	EHBP1	ENST00000405289.5	TSL:1	c.634+13915A>G		intron	N/A	ENSP00000385524.1	Q8NDI1-2

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

African (AFR) AF: 0.965 AC: 40040 AN: 41498

American (AMR) AF: 0.831 AC: 12686 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.943 AC: 3273 AN: 3470

East Asian (EAS) AF: 0.519 AC: 2685 AN: 5174

South Asian (SAS) AF: 0.633 AC: 3042 AN: 4808

European-Finnish (FIN) AF: 0.856 AC: 9018 AN: 10530

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57155 AN: 67962

Other (OTH) AF: 0.865 AC: 1830 AN: 2116

Alfa AF: 0.850 Hom.: 106637

Bravo AF: 0.866

Asia WGS AF: 0.533 AC: 1858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1877026; hg19: chr2-63072208;