chr9-69377283-C-T

Variant names:

• chr9-69377283-C-T
• rs41306153
• NM_001347995.2:c.712-87C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_001347995.2(ENTREP1):​c.712-87C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 848,110 control chromosomes in the GnomAD database, including 157 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.020 (43 hom., cov: 32)
  • Exomes 𝑓: 0.015 (114 hom.)
• Consequence: ENTREP1 NM_001347995.2 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.602
• Publications: 1 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=-1.02).
• BP6: Variant 9-69377283-C-T is Benign according to our data. Variant chr9-69377283-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1317981.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0199 (3021/152138) while in subpopulation AFR AF = 0.04 (1661/41488). AF 95% confidence interval is 0.0384. There are 43 homozygotes in GnomAd4. There are 1472 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 43 Unknown gene

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.712-87C>T		intron	N/A	NP_001334924.1	Q15884-4
	ENTREP1	NM_001127608.3		c.253-87C>T		intron	N/A	NP_001121080.1	Q15884-3
	ENTREP1	NM_004816.5		c.253-87C>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.712-87C>T		intron	N/A	ENSP00000304435.8	Q15884-4
	ENTREP1	ENST00000257515.12	TSL:1	c.253-87C>T		intron	N/A	ENSP00000257515.8	Q15884-3
	ENTREP1	ENST00000377216.4	TSL:1	n.253-87C>T		intron	N/A	ENSP00000366422.4	A0A0A0MRU1

Frequencies

GnomAD3 genomes AF: 0.0198 AC: 3006 AN: 152020 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.0397

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.000944

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0173

GnomAD4 exome AF: 0.0145 AC: 10092 AN: 695972 Hom.: 114 AF XY: 0.0152 AC XY: 5661 AN XY: 371716

African (AFR) AF: 0.0425 AC: 785 AN: 18480

American (AMR) AF: 0.00686 AC: 269 AN: 39190

Ashkenazi Jewish (ASJ) AF: 0.0120 AC: 249 AN: 20742

East Asian (EAS) AF: 0.0180 AC: 631 AN: 35058

South Asian (SAS) AF: 0.0266 AC: 1812 AN: 68232

European-Finnish (FIN) AF: 0.00208 AC: 106 AN: 50896

Middle Eastern (MID) AF: 0.0317 AC: 136 AN: 4286

European-Non Finnish (NFE) AF: 0.0130 AC: 5502 AN: 423752

Other (OTH) AF: 0.0170 AC: 602 AN: 35336

GnomAD4 genome AF: 0.0199 AC: 3021 AN: 152138 Hom.: 43 Cov.: 32 AF XY: 0.0198 AC XY: 1472 AN XY: 74380

African (AFR) AF: 0.0400 AC: 1661 AN: 41488

American (AMR) AF: 0.0126 AC: 192 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3470

East Asian (EAS) AF: 0.0161 AC: 83 AN: 5166

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4818

European-Finnish (FIN) AF: 0.000944 AC: 10 AN: 10592

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0128 AC: 872 AN: 68000

Other (OTH) AF: 0.0171 AC: 36 AN: 2102

Alfa AF: 0.0169 Hom.: 8

Bravo AF: 0.0220

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely 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	-1.0
CADD	Benign	0.36
DANN	Benign	0.70
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism

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: rs41306153; hg19: chr9-71992199;