rs10780326

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-69376112-C-G
• chr9-69376112-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001347995.2(ENTREP1):​c.711+248C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ENTREP1 NM_001347995.2 intron
• Clinical Significance: Not reported in ClinVar
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

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

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.7
DANN	Benign	0.72
PhyloP100		0.080

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;