chr9-69344250-C-T

Variant names:

• chr9-69344250-C-T
• rs7028837
• NM_001347995.2:c.471+7981C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001347995.2(ENTREP1):​c.471+7981C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,206 control chromosomes in the GnomAD database, including 48,141 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (48141 hom., cov: 32)
• Consequence: ENTREP1 NM_001347995.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTREP1	NM_001347995.2	c.471+7981C>T		intron_variant	Intron 2 of 10	ENST00000303068.14	NP_001334924.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTREP1	ENST00000303068.14	c.471+7981C>T		intron_variant	Intron 2 of 10	2	NM_001347995.2	ENSP00000304435.8
ENTREP1	ENST00000257515.12	c.12+7981C>T		intron_variant	Intron 2 of 10	1		ENSP00000257515.8
ENTREP1	ENST00000377216.4	n.12+7981C>T		intron_variant	Intron 2 of 9	1		ENSP00000366422.4
ENTREP1	ENST00000455972.6	c.12+7981C>T		intron_variant	Intron 2 of 10	5		ENSP00000395675.1

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120814 AN: 152088 Hom.: 48105 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.794 AC: 120902 AN: 152206 Hom.: 48141 Cov.: 32 AF XY: 0.797 AC XY: 59319 AN XY: 74406

African (AFR) AF: 0.822 AC: 34138 AN: 41550

American (AMR) AF: 0.782 AC: 11947 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3470

East Asian (EAS) AF: 0.703 AC: 3631 AN: 5168

South Asian (SAS) AF: 0.870 AC: 4202 AN: 4828

European-Finnish (FIN) AF: 0.847 AC: 8970 AN: 10592

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52780 AN: 68006

Other (OTH) AF: 0.772 AC: 1631 AN: 2114

Alfa AF: 0.794 Hom.: 6199

Bravo AF: 0.782

Asia WGS AF: 0.803 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.47
DANN	Benign	0.72
PhyloP100		-0.67
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: rs7028837; hg19: chr9-71959166;