Variant 9-69371889-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001347995.2(ENTREP1):c.582+280A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,074 control chromosomes in the GnomAD database, including 14,570 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 14570 hom., cov: 33)

Consequence

ENTREP1
NM_001347995.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.391

Variant links:

Genes affected

ENTREP1 (HGNC:24820): (endosomal transmembrane epsin interactor 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENTREP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 9-69371889-A-C is Benign according to our data. Variant chr9-69371889-A-C is described in ClinVar as [Benign]. Clinvar id is 1244511.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTREP1	NM_001347995.2 link	c.582+280A>C		intron_variant		ENST00000303068.14	NP_001334924.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTREP1	ENST00000303068.14 link	c.582+280A>C		intron_variant		2	NM_001347995.2	ENSP00000304435.8		Q15884-4

Frequencies

GnomAD3 genomes

AF:

0.429

AC:

65219

AN:

151956

Hom.:

14550

Cov.:

show subpopulations

Gnomad AFR

AF:

0.560

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.364

Gnomad SAS

AF:

0.452

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.380

Gnomad OTH

AF:

0.436

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

GnomAD4 genome

AF:

0.429

AC:

65280

AN:

152074

Hom.:

14570

Cov.:

AF XY:

0.429

AC XY:

31871

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.560

Gnomad4 AMR

AF:

0.347

Gnomad4 ASJ

AF:

0.380

Gnomad4 EAS

AF:

0.364

Gnomad4 SAS

AF:

0.452

Gnomad4 FIN

AF:

0.403

Gnomad4 NFE

AF:

0.380

Gnomad4 OTH

AF:

0.433

Alfa

AF:

0.384

Hom.:

19557

Bravo

AF:

0.431

Asia WGS

AF:

0.418

AC:

1454

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.72

DANN

Benign

0.77

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

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over