Variant 9-69376112-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.711+248C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,016 control chromosomes in the GnomAD database, including 14,489 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 14489 hom., cov: 32)

Consequence

ENTREP1
NM_001347995.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0800

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=-0.81).

BP6

Variant 9-69376112-C-T is Benign according to our data. Variant chr9-69376112-C-T is described in ClinVar as [Benign]. Clinvar id is 1259448.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTREP1	NM_001347995.2 link	c.711+248C>T		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.711+248C>T		intron_variant		2	NM_001347995.2	ENSP00000304435.8		Q15884-4

Frequencies

GnomAD3 genomes

AF:

0.428

AC:

65039

AN:

151898

Hom.:

14470

Cov.:

show subpopulations

Gnomad AFR

AF:

0.559

Gnomad AMI

AF:

0.338

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.363

Gnomad SAS

AF:

0.447

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.436

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

GnomAD4 genome

AF:

0.428

AC:

65098

AN:

152016

Hom.:

14489

Cov.:

AF XY:

0.428

AC XY:

31785

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.559

Gnomad4 AMR

AF:

0.347

Gnomad4 ASJ

AF:

0.383

Gnomad4 EAS

AF:

0.364

Gnomad4 SAS

AF:

0.447

Gnomad4 FIN

AF:

0.403

Gnomad4 NFE

AF:

0.378

Gnomad4 OTH

AF:

0.433

Alfa

AF:

0.394

Hom.:

2031

Bravo

AF:

0.430

Asia WGS

AF:

0.413

AC:

1436

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

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.1

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