rs3750552

Positions:

• chr9-69328086-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.414+2363C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 151,976 control chromosomes in the GnomAD database, including 38,897 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 0.71 (38897 hom., cov: 31)
• Consequence: ENTREP1 NM_001347995.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTREP1	NM_001347995.2	c.414+2363C>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.414+2363C>T		intron_variant		2	NM_001347995.2	ENSP00000304435	P1
ENTREP1	ENST00000377216.4	c.-46+3456C>T		intron_variant, NMD_transcript_variant		1		ENSP00000366422
ENTREP1	ENST00000455972.6	c.-46+3456C>T		intron_variant		5		ENSP00000395675

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108042 AN: 151858 Hom.: 38883 Cov.: 31

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.711 AC: 108099 AN: 151976 Hom.: 38897 Cov.: 31 AF XY: 0.714 AC XY: 53077 AN XY: 74292

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.709

Alfa AF: 0.728 Hom.: 6991

Bravo AF: 0.694

Asia WGS AF: 0.747 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.63

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: rs3750552; hg19: chr9-71943002;