chr9-69376112-C-T

Variant names:

• chr9-69376112-C-T
• rs10780326
• NM_001347995.2:c.711+248C>T

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.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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0800
• Publications: 3 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 (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 VariationId 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.

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.711+248C>T		intron	N/A	NP_001334924.1	Q15884-4
	ENTREP1	NM_001127608.3		c.252+248C>T		intron	N/A	NP_001121080.1	Q15884-3
	ENTREP1	NM_004816.5		c.252+248C>T		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.711+248C>T		intron	N/A	ENSP00000304435.8	Q15884-4
	ENTREP1	ENST00000257515.12	TSL:1	c.252+248C>T		intron	N/A	ENSP00000257515.8	Q15884-3
	ENTREP1	ENST00000377216.4	TSL:1	n.252+248C>T		intron	N/A	ENSP00000366422.4	A0A0A0MRU1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65039 AN: 151898 Hom.: 14470 Cov.: 32

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.: 32 AF XY: 0.428 AC XY: 31785 AN XY: 74306

African (AFR) AF: 0.559 AC: 23158 AN: 41450

American (AMR) AF: 0.347 AC: 5291 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1331 AN: 3472

East Asian (EAS) AF: 0.364 AC: 1878 AN: 5164

South Asian (SAS) AF: 0.447 AC: 2147 AN: 4806

European-Finnish (FIN) AF: 0.403 AC: 4260 AN: 10568

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25707 AN: 67974

Other (OTH) AF: 0.433 AC: 917 AN: 2116

Alfa AF: 0.398 Hom.: 2139

Bravo AF: 0.430

Asia WGS AF: 0.413 AC: 1436 AN: 3478

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	-0.81
CADD	Benign	8.1
DANN	Benign	0.77
PhyloP100		0.080
Mutation Taster		=100/0	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: rs10780326; hg19: chr9-71991028;