rs1471225

Positions:

• chr15-29596192-T-C

Variant summary

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

The NM_001387215.1(ENTREP2):​c.-70+78907A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,056 control chromosomes in the GnomAD database, including 17,943 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 0.48 (17943 hom., cov: 32)
• Consequence: ENTREP2 NM_001387215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980

Genes affected

ENTREP2 (HGNC:29075): (endosomal transmembrane epsin interactor 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTREP2	NM_001387215.1	c.-70+78907A>G		intron_variant			NP_001374144.1
ENTREP2	NM_001387216.1	c.-70+78907A>G		intron_variant			NP_001374145.1
ENTREP2	NM_001387217.1	c.-70+78907A>G		intron_variant			NP_001374146.1
		n.29596192T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72911 AN: 151938 Hom.: 17929 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.480 AC: 72961 AN: 152056 Hom.: 17943 Cov.: 32 AF XY: 0.475 AC XY: 35274 AN XY: 74314

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.499

Alfa AF: 0.521 Hom.: 22392

Bravo AF: 0.472

Asia WGS AF: 0.458 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1471225; hg19: chr15-29888396;