NM_015307.2:c.631-2785A>G

Variant names:

• chr15-29139979-T-C
• rs11634779
• NM_015307.2:c.631-2785A>G

Variant summary

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

The NM_015307.2(ENTREP2):​c.631-2785A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,140 control chromosomes in the GnomAD database, including 7,889 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 0.29 (7889 hom., cov: 33)
• Consequence: ENTREP2 NM_015307.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10
• Publications: 3 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTREP2	NM_015307.2	c.631-2785A>G		intron_variant	Intron 5 of 10	ENST00000261275.5	NP_056122.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTREP2	ENST00000261275.5	c.631-2785A>G		intron_variant	Intron 5 of 10	5	NM_015307.2	ENSP00000261275.4
ENTREP2	ENST00000560021.1	n.367-2785A>G		intron_variant	Intron 2 of 7	1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44092 AN: 152022 Hom.: 7892 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.0683

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.290 AC: 44084 AN: 152140 Hom.: 7889 Cov.: 33 AF XY: 0.288 AC XY: 21411 AN XY: 74372

African (AFR) AF: 0.112 AC: 4659 AN: 41544

American (AMR) AF: 0.243 AC: 3714 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1420 AN: 3472

East Asian (EAS) AF: 0.0683 AC: 352 AN: 5156

South Asian (SAS) AF: 0.200 AC: 965 AN: 4826

European-Finnish (FIN) AF: 0.458 AC: 4850 AN: 10592

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26973 AN: 67940

Other (OTH) AF: 0.298 AC: 629 AN: 2112

Alfa AF: 0.357 Hom.: 4634

Bravo AF: 0.267

Asia WGS AF: 0.114 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.71
PhyloP100		2.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11634779; hg19: chr15-29432182;