rs8031323

Variant names:

• chr15-29582546-G-A
• rs8031323
• NM_001387215.1:c.-70+92553C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387215.1(ENTREP2):​c.-70+92553C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,974 control chromosomes in the GnomAD database, including 21,951 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 0.51 (21951 hom., cov: 34)
• Consequence: ENTREP2 NM_001387215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387215.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTREP2	NM_001387215.1		c.-70+92553C>T		intron	N/A	NP_001374144.1
	ENTREP2	NM_001387216.1		c.-70+92553C>T		intron	N/A	NP_001374145.1
	ENTREP2	NM_001387217.1		c.-70+92553C>T		intron	N/A	NP_001374146.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77297 AN: 151856 Hom.: 21938 Cov.: 34

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.509 AC: 77333 AN: 151974 Hom.: 21951 Cov.: 34 AF XY: 0.503 AC XY: 37338 AN XY: 74262

African (AFR) AF: 0.276 AC: 11470 AN: 41484

American (AMR) AF: 0.490 AC: 7488 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3472

East Asian (EAS) AF: 0.215 AC: 1113 AN: 5166

South Asian (SAS) AF: 0.489 AC: 2355 AN: 4816

European-Finnish (FIN) AF: 0.617 AC: 6479 AN: 10502

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44359 AN: 67946

Other (OTH) AF: 0.556 AC: 1173 AN: 2108

Alfa AF: 0.603 Hom.: 105362

Bravo AF: 0.492

Asia WGS AF: 0.411 AC: 1426 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	3.1
DANN	Benign	0.77
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs8031323; hg19: chr15-29874750;