Variant 9-69375729-C-T 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.583-7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 1,600,520 control chromosomes in the GnomAD database, including 131,948 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.33 ( 9883 hom., cov: 31)

Exomes 𝑓: 0.40 ( 122065 hom. )

Consequence

ENTREP1
NM_001347995.2 splice_region, intron

Scores

Splicing: ADA: 0.00009496

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.702

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:

ENTREP1 (HGNC:):

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=-0.81).

BP6

Variant 9-69375729-C-T is Benign according to our data. Variant chr9-69375729-C-T is described in ClinVar as [Benign]. Clinvar id is 508095.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTREP1	NM_001347995.2 linkuse as main transcript	c.583-7C>T		splice_region_variant, intron_variant		ENST00000303068.14	NP_001334924.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTREP1	ENST00000303068.14 linkuse as main transcript	c.583-7C>T		splice_region_variant, intron_variant		2	NM_001347995.2	ENSP00000304435.8		Q15884-4

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50349

AN:

151704

Hom.:

9876

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.386

Gnomad AMR

AF:

0.409

Gnomad ASJ

AF:

0.393

Gnomad EAS

AF:

0.375

Gnomad SAS

AF:

0.417

Gnomad FIN

AF:

0.446

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.415

Gnomad OTH

AF:

0.321

GnomAD3 exomes

AF:

0.401

AC:

100467

AN:

250336

Hom.:

21399

AF XY:

0.403

AC XY:

54472

AN XY:

135298

show subpopulations

Gnomad AFR exome

AF:

0.113

Gnomad AMR exome

AF:

0.511

Gnomad ASJ exome

AF:

0.383

Gnomad EAS exome

AF:

0.374

Gnomad SAS exome

AF:

0.427

Gnomad FIN exome

AF:

0.441

Gnomad NFE exome

AF:

0.402

Gnomad OTH exome

AF:

0.381

GnomAD4 exome

AF:

0.405

AC:

586415

AN:

1448698

Hom.:

122065

Cov.:

AF XY:

0.405

AC XY:

292508

AN XY:

721448

show subpopulations

Gnomad4 AFR exome

AF:

0.102

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.387

Gnomad4 EAS exome

AF:

0.396

Gnomad4 SAS exome

AF:

0.426

Gnomad4 FIN exome

AF:

0.449

Gnomad4 NFE exome

AF:

0.409

Gnomad4 OTH exome

AF:

0.381

GnomAD4 genome

AF:

0.332

AC:

50368

AN:

151822

Hom.:

9883

Cov.:

AF XY:

0.336

AC XY:

24913

AN XY:

74162

show subpopulations

Gnomad4 AFR

AF:

0.117

Gnomad4 AMR

AF:

0.410

Gnomad4 ASJ

AF:

0.393

Gnomad4 EAS

AF:

0.375

Gnomad4 SAS

AF:

0.417

Gnomad4 FIN

AF:

0.446

Gnomad4 NFE

AF:

0.415

Gnomad4 OTH

AF:

0.323

Alfa

AF:

0.389

Hom.:

22535

Bravo

AF:

0.314

Asia WGS

AF:

0.376

AC:

1304

AN:

3478

EpiCase

AF:

0.389

EpiControl

AF:

0.383

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 09, 2017

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.0

DANN

Benign

0.33

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000095

dbscSNV1_RF

Benign

0.0020

SpliceAI score (max)

0.010

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