9-69371399-T-C

Position:

• chr9-69371399-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001347995.2(ENTREP1):​c.472-100T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 886,708 control chromosomes in the GnomAD database, including 288,308 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.81 (50224 hom., cov: 32)
  • Exomes 𝑓: 0.80 (238084 hom.)
• Consequence: ENTREP1 NM_001347995.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.230

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=-0.88).
• BP6: Variant 9-69371399-T-C is Benign according to our data. Variant chr9-69371399-T-C is described in ClinVar as [Benign]. Clinvar id is 1242940.Status of the report is criteria_provided_single_submitter, 1 stars.
• 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/exons	MANE	Protein	UniProt
ENTREP1	NM_001347995.2	c.472-100T>C		intron_variant		ENST00000303068.14	NP_001334924.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTREP1	ENST00000303068.14	c.472-100T>C		intron_variant		2	NM_001347995.2	ENSP00000304435.8

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123408 AN: 151954 Hom.: 50174 Cov.: 32

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.797

GnomAD3 exomes AF: 0.804 AC: 195868 AN: 243730 Hom.: 78957 AF XY: 0.805 AC XY: 106175 AN XY: 131916

Gnomad AFR exome AF: 0.855

Gnomad AMR exome AF: 0.803

Gnomad ASJ exome AF: 0.773

Gnomad EAS exome AF: 0.729

Gnomad SAS exome AF: 0.864

Gnomad FIN exome AF: 0.809

Gnomad NFE exome AF: 0.795

Gnomad OTH exome AF: 0.780

GnomAD4 exome AF: 0.804 AC: 590692 AN: 734638 Hom.: 238084 Cov.: 10 AF XY: 0.806 AC XY: 317244 AN XY: 393726

Gnomad4 AFR exome AF: 0.852

Gnomad4 AMR exome AF: 0.805

Gnomad4 ASJ exome AF: 0.773

Gnomad4 EAS exome AF: 0.776

Gnomad4 SAS exome AF: 0.860

Gnomad4 FIN exome AF: 0.818

Gnomad4 NFE exome AF: 0.797

Gnomad4 OTH exome AF: 0.792

GnomAD4 genome AF: 0.812 AC: 123517 AN: 152070 Hom.: 50224 Cov.: 32 AF XY: 0.813 AC XY: 60433 AN XY: 74336

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.797

Alfa AF: 0.780 Hom.: 5095

Bravo AF: 0.806

Asia WGS AF: 0.798 AC: 2776 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.81
DANN	Benign	0.43

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: rs1034239; hg19: chr9-71986315;