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GeneBe

rs721048

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5BP4BA1

The NM_001142616.3(EHBP1):c.1185+30064G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,112 control chromosomes in the GnomAD database, including 1,698 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: 𝑓 0.13 ( 1698 hom., cov: 31)

Consequence

EHBP1
NM_001142616.3 intron

Scores

2

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 0.575
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PP5
Variant 2-62904596-G-A is Pathogenic according to our data. Variant chr2-62904596-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 1364.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).. Strength limited to SUPPORTING due to the PP5.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EHBP1NM_001142616.3 linkuse as main transcriptc.1185+30064G>A intron_variant ENST00000431489.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EHBP1ENST00000431489.6 linkuse as main transcriptc.1185+30064G>A intron_variant 1 NM_001142616.3 A1Q8NDI1-3
EHBP1ENST00000263991.9 linkuse as main transcriptc.1290+30064G>A intron_variant 1 P3Q8NDI1-1
EHBP1ENST00000405289.5 linkuse as main transcriptc.1185+30064G>A intron_variant 1 A1Q8NDI1-2
EHBP1ENST00000405015.7 linkuse as main transcriptc.1185+30064G>A intron_variant 2 A1Q8NDI1-3

Frequencies

GnomAD3 genomes
AF:
0.133
AC:
20219
AN:
151994
Hom.:
1697
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0366
Gnomad AMI
AF:
0.181
Gnomad AMR
AF:
0.185
Gnomad ASJ
AF:
0.159
Gnomad EAS
AF:
0.0477
Gnomad SAS
AF:
0.100
Gnomad FIN
AF:
0.155
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.183
Gnomad OTH
AF:
0.161
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.133
AC:
20208
AN:
152112
Hom.:
1698
Cov.:
31
AF XY:
0.133
AC XY:
9868
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.0365
Gnomad4 AMR
AF:
0.184
Gnomad4 ASJ
AF:
0.159
Gnomad4 EAS
AF:
0.0476
Gnomad4 SAS
AF:
0.100
Gnomad4 FIN
AF:
0.155
Gnomad4 NFE
AF:
0.183
Gnomad4 OTH
AF:
0.160
Alfa
AF:
0.173
Hom.:
2478
Bravo
AF:
0.132
Asia WGS
AF:
0.0820
AC:
285
AN:
3478

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Prostate cancer, hereditary, 12 Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMMar 01, 2008- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
1.4
Dann
Benign
0.90

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs721048; hg19: chr2-63131731; COSMIC: COSV50416374; API