rs1037782

chr15-29614744-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+60355A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,090 control chromosomes in the GnomAD database, including 2,749 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 0.17 (2749 hom., cov: 33)
• Consequence: ENTREP2 NM_001387215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

ENTREP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTREP2	NM_001387215.1	c.-70+60355A>G		intron_variant
ENTREP2	NM_001387216.1	c.-70+60355A>G		intron_variant
ENTREP2	NM_001387217.1	c.-70+60355A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25264 AN: 151972 Hom.: 2738 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.166 AC: 25306 AN: 152090 Hom.: 2749 Cov.: 33 AF XY: 0.165 AC XY: 12241 AN XY: 74364

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.0574

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.173

Alfa AF: 0.0604 Hom.: 82

Bravo AF: 0.176

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.82
Dann	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1037782; hg19: chr15-29906948;