rs1037782

Variant names:

• chr15-29614744-T-C
• rs1037782
• NM_001387215.1:c.-70+60355A>G

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+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
• Publications: 1 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 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+60355A>G		intron	N/A	NP_001374144.1
	ENTREP2	NM_001387216.1		c.-70+60355A>G		intron	N/A	NP_001374145.1
	ENTREP2	NM_001387217.1		c.-70+60355A>G		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: 0.166 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

African (AFR) AF: 0.305 AC: 12660 AN: 41488

American (AMR) AF: 0.115 AC: 1763 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3470

East Asian (EAS) AF: 0.168 AC: 869 AN: 5162

South Asian (SAS) AF: 0.230 AC: 1110 AN: 4816

European-Finnish (FIN) AF: 0.0574 AC: 607 AN: 10580

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.108 AC: 7350 AN: 67982

Other (OTH) AF: 0.173 AC: 365 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.82
DANN	Benign	0.12
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1037782; hg19: chr15-29906948;