9-69371400-G-A

Variant names:

• chr9-69371400-G-A
• rs1034238
• NM_001347995.2:c.472-99G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.169
• Publications: 4 publications found

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)

ACMG classification

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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.: 32

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

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.: 10 AF XY: 0.411 AC XY: 162198 AN XY: 395012

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

GnomAD4 genome AF: 0.383 AC: 58200 AN: 151970 Hom.: 11467 Cov.: 32 AF XY: 0.385 AC XY: 28588 AN XY: 74260

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: 87 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28145 AN: 67918

Other (OTH) AF: 0.357 AC: 752 AN: 2108

Alfa AF: 0.406 Hom.: 4029

Bravo AF: 0.373

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.49
DANN	Benign	0.47
PhyloP100		-0.17
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1034238; hg19: chr9-71986316; COSMIC: COSV57385649; COSMIC: COSV57385649;