rs7028837

Positions:

• chr9-69344250-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001347995.2(ENTREP1):​c.471+7981C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,206 control chromosomes in the GnomAD database, including 48,141 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (48141 hom., cov: 32)
• Consequence: ENTREP1 NM_001347995.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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.471+7981C>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.471+7981C>T		intron_variant		2	NM_001347995.2	ENSP00000304435.8
ENTREP1	ENST00000257515.12	c.12+7981C>T		intron_variant		1		ENSP00000257515.8
ENTREP1	ENST00000377216.4	n.12+7981C>T		intron_variant		1		ENSP00000366422.4
ENTREP1	ENST00000455972.6	c.12+7981C>T		intron_variant		5		ENSP00000395675.1

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120814 AN: 152088 Hom.: 48105 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.769

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.794 AC: 120902 AN: 152206 Hom.: 48141 Cov.: 32 AF XY: 0.797 AC XY: 59319 AN XY: 74406

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.772

Alfa AF: 0.793 Hom.: 5942

Bravo AF: 0.782

Asia WGS AF: 0.803 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.47
DANN	Benign	0.72

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: rs7028837; hg19: chr9-71959166;