Variant rs721048 details in Genebe, Genetics Data Aggregator

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 151994 control chromosomes in the gnomAD Genomes database, including 1697 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 ( 1697 hom., cov: 31)

Consequence

EHBP1
NM_001142616.3 intron

Scores

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 0.575

Links

EHBP1 (HGNC:29144):

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

GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EHBP1	NM_001142616.3 linkuse as main transcript	c.1185+30064G>A		intron_variant		ENST00000431489.6

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
EHBP1	ENST00000431489.6 linkuse as main transcript	c.1185+30064G>A	intron_variant	1	NM_001142616.3	A1	Q8NDI1-3
EHBP1	ENST00000263991.9 linkuse as main transcript	c.1290+30064G>A	intron_variant	1		P3	Q8NDI1-1
EHBP1	ENST00000405289.5 linkuse as main transcript	c.1185+30064G>A	intron_variant	1		A1	Q8NDI1-2
EHBP1	ENST00000405015.7 linkuse as main transcript	c.1185+30064G>A	intron_variant	2		A1	Q8NDI1-3

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20219

AN:

151994

Hom.:

1697

Cov.:

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

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 provided

literature only

OMIM

Mar 01, 2008

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

Cadd

Benign

2.5

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over