chr9-69385787-TA-T

Position:

• chr9-69385787-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001347995.2(ENTREP1):​c.1163-5delA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0381 in 934,706 control chromosomes in the GnomAD database, including 1,826 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.090 (238 hom., cov: 0)
  • Exomes 𝑓: 0.035 (1588 hom.)
• Consequence: ENTREP1 NM_001347995.2 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter U:1 B:1
• Conservation: PhyloP100: -1.11

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 -10 ACMG points.

• BP6: Variant 9-69385787-TA-T is Benign according to our data. Variant chr9-69385787-TA-T is described in ClinVar as [Benign]. Clinvar id is 161521.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTREP1	NM_001347995.2	c.1163-5delA		splice_region_variant, intron_variant		ENST00000303068.14	NP_001334924.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTREP1	ENST00000303068.14	c.1163-5delA		splice_region_variant, intron_variant		2	NM_001347995.2	ENSP00000304435.8

Frequencies

GnomAD3 genomes AF: 0.0901 AC: 4664 AN: 51782 Hom.: 239 Cov.: 0

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0897

Gnomad AMR AF: 0.0499

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.0336

Gnomad SAS AF: 0.0770

Gnomad FIN AF: 0.0678

Gnomad MID AF: 0.0859

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.0905

GnomAD3 exomes AF: 0.122 AC: 5020 AN: 41060 Hom.: 1126 AF XY: 0.113 AC XY: 2381 AN XY: 21102

Gnomad AFR exome AF: 0.123

Gnomad AMR exome AF: 0.0603

Gnomad ASJ exome AF: 0.0681

Gnomad EAS exome AF: 0.0600

Gnomad SAS exome AF: 0.0561

Gnomad FIN exome AF: 0.219

Gnomad NFE exome AF: 0.130

Gnomad OTH exome AF: 0.0844

GnomAD4 exome AF: 0.0350 AC: 30931 AN: 882894 Hom.: 1588 Cov.: 34 AF XY: 0.0366 AC XY: 15509 AN XY: 423402

Gnomad4 AFR exome AF: 0.0655

Gnomad4 AMR exome AF: 0.0472

Gnomad4 ASJ exome AF: 0.0485

Gnomad4 EAS exome AF: 0.0342

Gnomad4 SAS exome AF: 0.0843

Gnomad4 FIN exome AF: 0.135

Gnomad4 NFE exome AF: 0.0282

Gnomad4 OTH exome AF: 0.0377

GnomAD4 genome AF: 0.0902 AC: 4673 AN: 51812 Hom.: 238 Cov.: 0 AF XY: 0.0928 AC XY: 2303 AN XY: 24810

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0498

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.0334

Gnomad4 SAS AF: 0.0752

Gnomad4 FIN AF: 0.0678

Gnomad4 NFE AF: 0.0629

Gnomad4 OTH AF: 0.0904

ClinVar

Significance: Benign

Submissions summary: Uncertain:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Malignant tumor of prostate Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

Science for Life laboratory, Karolinska Institutet

-

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 01, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs193921010; hg19: chr9-72000703;