9-69377283-C-T

Position:

• chr9-69377283-C-T

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 id 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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 43 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTREP1	NM_001347995.2	c.712-87C>T		intron_variant		ENST00000303068.14	NP_001334924.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTREP1	ENST00000303068.14	c.712-87C>T		intron_variant		2	NM_001347995.2	ENSP00000304435.8

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

Gnomad4 AFR exome AF: 0.0425

Gnomad4 AMR exome AF: 0.00686

Gnomad4 ASJ exome AF: 0.0120

Gnomad4 EAS exome AF: 0.0180

Gnomad4 SAS exome AF: 0.0266

Gnomad4 FIN exome AF: 0.00208

Gnomad4 NFE exome AF: 0.0130

Gnomad4 OTH exome AF: 0.0170

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

Gnomad4 AFR AF: 0.0400

Gnomad4 AMR AF: 0.0126

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.0161

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.000944

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0171

Alfa AF: 0.0158 Hom.: 6

Bravo AF: 0.0220

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 01, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs41306153; hg19: chr9-71992199;