chr15-29582546-G-A

Position:

• chr15-29582546-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENTREP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTREP2	NM_001387215.1	c.-70+92553C>T		intron_variant			NP_001374144.1
ENTREP2	NM_001387216.1	c.-70+92553C>T		intron_variant			NP_001374145.1
ENTREP2	NM_001387217.1	c.-70+92553C>T		intron_variant			NP_001374146.1

Ensembl

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

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

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.556

Alfa AF: 0.627 Hom.: 43231

Bravo AF: 0.492

Asia WGS AF: 0.411 AC: 1426 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8031323; hg19: chr15-29874750;