chr2-62691943-T-C

Variant names:

• chr2-62691943-T-C
• rs360794
• NM_001142615.3:c.-295-14954T>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.-295-14954T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,166 control chromosomes in the GnomAD database, including 2,161 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 (2161 hom., cov: 32)
• Consequence: EHBP1 NM_001142615.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• 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=-0.92).
• 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.-295-14954T>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.-295-14954T>C		intron	N/A	ENSP00000384143.3	Q8NDI1-3
	EHBP1	ENST00000413434.5	TSL:4	c.8+17850T>C		intron	N/A	ENSP00000392192.1	C9IYU2
	EHBP1	ENST00000449820.5	TSL:5	c.-49+17860T>C		intron	N/A	ENSP00000399609.1	C9K0H9

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23941 AN: 152048 Hom.: 2157 Cov.: 32

Gnomad AFR AF: 0.0839

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0861

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.158 AC: 23971 AN: 152166 Hom.: 2161 Cov.: 32 AF XY: 0.158 AC XY: 11786 AN XY: 74396

African (AFR) AF: 0.0842 AC: 3496 AN: 41532

American (AMR) AF: 0.129 AC: 1971 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 838 AN: 3472

East Asian (EAS) AF: 0.0867 AC: 450 AN: 5190

South Asian (SAS) AF: 0.148 AC: 713 AN: 4830

European-Finnish (FIN) AF: 0.215 AC: 2272 AN: 10566

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

European-Non Finnish (NFE) AF: 0.201 AC: 13660 AN: 67976

Other (OTH) AF: 0.171 AC: 361 AN: 2112

Alfa AF: 0.182 Hom.: 1092

Bravo AF: 0.146

Asia WGS AF: 0.108 AC: 375 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.38
PhyloP100		-0.039
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: rs360794; hg19: chr2-62919078;