rs360795

chr2-62692199-G-C

Variant summary

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

The NM_001142615.3(EHBP1):c.-295-14698G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,182 control chromosomes in the GnomAD database, including 2,131 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 0.16 (2131 hom., cov: 32)
• Consequence: EHBP1 NM_001142615.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EHBP1	NM_001142615.3	c.-295-14698G>C		intron_variant
EHBP1	XM_011532718.4	c.-257+18116G>C		intron_variant
EHBP1	XM_047443744.1	c.-295-14698G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EHBP1	ENST00000405015.7	c.-295-14698G>C		intron_variant		2		A1
EHBP1	ENST00000413434.5	c.8+18106G>C		intron_variant		4
EHBP1	ENST00000426940.5	c.-257+18116G>C		intron_variant		4
EHBP1	ENST00000449820.5	c.-49+18116G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23766 AN: 152064 Hom.: 2128 Cov.: 32

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0858

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.156 AC: 23785 AN: 152182 Hom.: 2131 Cov.: 32 AF XY: 0.157 AC XY: 11695 AN XY: 74384

Gnomad4 AFR AF: 0.0807

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.0864

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.168

Alfa AF: 0.179 Hom.: 342

Bravo AF: 0.145

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs360795; hg19: chr2-62919334;