Genetic Variant ENTREP1:c.472-99G>A (chr9-69371400-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001347995.2(ENTREP1):c.472-99G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 889,762 control chromosomes in the GnomAD database, including 75,446 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.38 ( 11467 hom., cov: 32)

Exomes 𝑓: 0.41 ( 63979 hom. )

Consequence

ENTREP1
NM_001347995.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.169

Publications

4 publications found

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 Gene-Disease associations (from GenCC):

schizophrenia
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ENTREP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.015).

BP6

Variant 9-69371400-G-A is Benign according to our data. Variant chr9-69371400-G-A is described in ClinVar as Benign. ClinVar VariationId is 1280255.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001347995.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENTREP1	NM_001347995.2	MANE Select	c.472-99G>A	intron	N/A	NP_001334924.1	Q15884-4
ENTREP1	NM_001127608.3		c.13-99G>A	intron	N/A	NP_001121080.1	Q15884-3
ENTREP1	NM_004816.5		c.13-99G>A	intron	N/A	NP_004807.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENTREP1	ENST00000303068.14	TSL:2 MANE Select	c.472-99G>A	intron	N/A	ENSP00000304435.8	Q15884-4
ENTREP1	ENST00000257515.12	TSL:1	c.13-99G>A	intron	N/A	ENSP00000257515.8	Q15884-3
ENTREP1	ENST00000377216.4	TSL:1	n.13-99G>A	intron	N/A	ENSP00000366422.4	A0A0A0MRU1

Frequencies

GnomAD3 genomes

AF:

0.383

AC:

58153

AN:

151854

Hom.:

11459

Cov.:

show subpopulations

Gnomad AFR

AF:

0.298

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.433

Gnomad ASJ

AF:

0.394

Gnomad EAS

AF:

0.360

Gnomad SAS

AF:

0.412

Gnomad FIN

AF:

0.445

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.414

Gnomad OTH

AF:

0.354

GnomAD2 exomes

AF:

0.412

AC:

100408

AN:

243590

AF XY:

0.409

show subpopulations

Gnomad AFR exome

AF:

0.294

Gnomad AMR exome

AF:

0.518

Gnomad ASJ exome

AF:

0.381

Gnomad EAS exome

AF:

0.360

Gnomad FIN exome

AF:

0.440

Gnomad NFE exome

AF:

0.401

Gnomad OTH exome

AF:

0.388

GnomAD4 exome

AF:

0.411

AC:

303477

AN:

737792

Hom.:

63979

Cov.:

AF XY:

0.411

AC XY:

162198

AN XY:

395012

show subpopulations

African (AFR)

AF:

0.285

AC:

5534

AN:

19434

American (AMR)

AF:

0.510

AC:

21880

AN:

42866

Ashkenazi Jewish (ASJ)

AF:

0.385

AC:

8272

AN:

21498

East Asian (EAS)

AF:

0.386

AC:

14050

AN:

36382

South Asian (SAS)

AF:

0.422

AC:

29917

AN:

70892

European-Finnish (FIN)

AF:

0.449

AC:

23546

AN:

52404

Middle Eastern (MID)

AF:

0.334

AC:

1453

AN:

4356

European-Non Finnish (NFE)

AF:

0.407

AC:

184533

AN:

453404

Other (OTH)

AF:

0.391

AC:

14292

AN:

36556

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

8065

16130

24196

32261

40326

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2672

5344

8016

10688

13360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.383

AC:

58200

AN:

151970

Hom.:

11467

Cov.:

AF XY:

0.385

AC XY:

28588

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.298

AC:

12348

AN:

41470

American (AMR)

AF:

0.433

AC:

6606

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.394

AC:

1365

AN:

3468

East Asian (EAS)

AF:

0.361

AC:

1870

AN:

5184

South Asian (SAS)

AF:

0.412

AC:

1984

AN:

4820

European-Finnish (FIN)

AF:

0.445

AC:

4694

AN:

10540

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.414

AC:

28145

AN:

67918

Other (OTH)

AF:

0.357

AC:

752

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1850

3700

5549

7399

9249

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

578

1156

1734

2312

2890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.406

Hom.:

4029

Bravo

AF:

0.373

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.49

(source)

DANN

Benign

0.47

PhyloP100

-0.17

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over