chr9-69371360-G-C

Position:

• chr9-69371360-G-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.472-139G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 770,964 control chromosomes in the GnomAD database, including 2,682 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.085 (559 hom., cov: 33)
  • Exomes 𝑓: 0.080 (2123 hom.)
• Consequence: ENTREP1 NM_001347995.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.51

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=-0.77).
• BP6: Variant 9-69371360-G-C is Benign according to our data. Variant chr9-69371360-G-C is described in ClinVar as [Benign]. Clinvar id is 1281258.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTREP1	NM_001347995.2	c.472-139G>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.472-139G>C		intron_variant		2	NM_001347995.2	ENSP00000304435.8

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12932 AN: 152110 Hom.: 559 Cov.: 33

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.0732

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0828

Gnomad OTH AF: 0.0969

GnomAD3 exomes AF: 0.0756 AC: 15728 AN: 207908 Hom.: 667 AF XY: 0.0755 AC XY: 8509 AN XY: 112736

Gnomad AFR exome AF: 0.0955

Gnomad AMR exome AF: 0.0477

Gnomad ASJ exome AF: 0.0971

Gnomad EAS exome AF: 0.0567

Gnomad SAS exome AF: 0.0691

Gnomad FIN exome AF: 0.0736

Gnomad NFE exome AF: 0.0849

Gnomad OTH exome AF: 0.0819

GnomAD4 exome AF: 0.0801 AC: 49578 AN: 618736 Hom.: 2123 Cov.: 7 AF XY: 0.0796 AC XY: 26718 AN XY: 335784

Gnomad4 AFR exome AF: 0.0991

Gnomad4 AMR exome AF: 0.0521

Gnomad4 ASJ exome AF: 0.0992

Gnomad4 EAS exome AF: 0.0683

Gnomad4 SAS exome AF: 0.0662

Gnomad4 FIN exome AF: 0.0775

Gnomad4 NFE exome AF: 0.0851

Gnomad4 OTH exome AF: 0.0843

GnomAD4 genome AF: 0.0850 AC: 12942 AN: 152228 Hom.: 559 Cov.: 33 AF XY: 0.0839 AC XY: 6242 AN XY: 74410

Gnomad4 AFR AF: 0.0984

Gnomad4 AMR AF: 0.0731

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0601

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.0767

Gnomad4 NFE AF: 0.0828

Gnomad4 OTH AF: 0.0964

Alfa AF: 0.0530 Hom.: 54

Bravo AF: 0.0872

Asia WGS AF: 0.0700 AC: 243 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 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.31
DANN	Benign	0.79

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: rs74709394; hg19: chr9-71986276;