15-29136814-G-C

Variant names:

• chr15-29136814-G-C
• rs7167473
• NM_015307.2:c.791+220C>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.791+220C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,042 control chromosomes in the GnomAD database, including 10,512 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 0.35 (10512 hom., cov: 32)
• Consequence: ENTREP2 NM_015307.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015307.2. 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_015307.2	MANE Select	c.791+220C>G		intron	N/A	NP_056122.1
	ENTREP2	NM_001387214.1		c.656+220C>G		intron	N/A	NP_001374143.1
	ENTREP2	NM_001387215.1		c.503+220C>G		intron	N/A	NP_001374144.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTREP2	ENST00000261275.5	TSL:5 MANE Select	c.791+220C>G		intron	N/A	ENSP00000261275.4
	ENTREP2	ENST00000560021.1	TSL:1	n.527+220C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52670 AN: 151924 Hom.: 10515 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.346 AC: 52658 AN: 152042 Hom.: 10512 Cov.: 32 AF XY: 0.343 AC XY: 25478 AN XY: 74328

African (AFR) AF: 0.192 AC: 7949 AN: 41466

American (AMR) AF: 0.256 AC: 3913 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3472

East Asian (EAS) AF: 0.106 AC: 548 AN: 5176

South Asian (SAS) AF: 0.213 AC: 1024 AN: 4818

European-Finnish (FIN) AF: 0.549 AC: 5800 AN: 10564

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30585 AN: 67954

Other (OTH) AF: 0.330 AC: 696 AN: 2106

Alfa AF: 0.268 Hom.: 730

Bravo AF: 0.320

Asia WGS AF: 0.144 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.039
DANN	Benign	0.49
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7167473; hg19: chr15-29429017; COSMIC: COSV54273830;