rs7591708

Variant names:

• chr2-62794915-T-C
• rs7591708
• NM_001142616.3:c.312+23523T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-62794915-T-C
• chr2-62794915-T-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.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
• Publications: 2 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EHBP1	NM_001142616.3	MANE Select	c.312+23523T>C		intron	N/A	NP_001136088.1
	EHBP1	NM_001354212.1		c.312+23523T>C		intron	N/A	NP_001341141.1
	EHBP1	NM_001354213.1		c.312+23523T>C		intron	N/A	NP_001341142.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EHBP1	ENST00000431489.6	TSL:1 MANE Select	c.312+23523T>C		intron	N/A	ENSP00000403783.1
	EHBP1	ENST00000263991.9	TSL:1	c.312+23523T>C		intron	N/A	ENSP00000263991.5
	EHBP1	ENST00000405289.5	TSL:1	c.312+23523T>C		intron	N/A	ENSP00000385524.1

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

African (AFR) AF: 0.575 AC: 23833 AN: 41438

American (AMR) AF: 0.625 AC: 9526 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2696 AN: 3466

East Asian (EAS) AF: 0.465 AC: 2394 AN: 5152

South Asian (SAS) AF: 0.511 AC: 2462 AN: 4822

European-Finnish (FIN) AF: 0.666 AC: 7028 AN: 10558

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.642 AC: 43519 AN: 67818

Other (OTH) AF: 0.641 AC: 1349 AN: 2106

Alfa AF: 0.622 Hom.: 14488

Bravo AF: 0.618

Asia WGS AF: 0.420 AC: 1462 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	5.3
DANN	Benign	0.79
PhyloP100		-0.68
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: rs7591708; hg19: chr2-63022050;