chr2-62692199-G-C

Variant names:

• chr2-62692199-G-C
• rs360795
• NM_001142615.3:c.-295-14698G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142615.3. 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_001142615.3		c.-295-14698G>C		intron	N/A	NP_001136087.1	Q8NDI1-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EHBP1	ENST00000405015.7	TSL:2	c.-295-14698G>C		intron	N/A	ENSP00000384143.3	Q8NDI1-3
	EHBP1	ENST00000413434.5	TSL:4	c.8+18106G>C		intron	N/A	ENSP00000392192.1	C9IYU2
	EHBP1	ENST00000449820.5	TSL:5	c.-49+18116G>C		intron	N/A	ENSP00000399609.1	C9K0H9

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

African (AFR) AF: 0.0807 AC: 3352 AN: 41542

American (AMR) AF: 0.128 AC: 1962 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3466

East Asian (EAS) AF: 0.0864 AC: 448 AN: 5184

South Asian (SAS) AF: 0.147 AC: 708 AN: 4822

European-Finnish (FIN) AF: 0.215 AC: 2275 AN: 10588

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13642 AN: 67974

Other (OTH) AF: 0.168 AC: 356 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.36
PhyloP100		-0.080
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs360795; hg19: chr2-62919334;