rs16892786

Variant names:

• chr8-119570631-T-C
• rs16892786
• NM_001040092.3:c.1917+74A>G

Variant summary

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

The NM_001040092.3(ENPP2):​c.1917+74A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 777,548 control chromosomes in the GnomAD database, including 5,785 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 0.12 (1182 hom., cov: 32)
  • Exomes 𝑓: 0.12 (4603 hom.)
• Consequence: ENPP2 NM_001040092.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 6 publications found

Genes affected

ENPP2 (HGNC:3357): (ectonucleotide pyrophosphatase/phosphodiesterase 2) The protein encoded by this gene functions as both a phosphodiesterase, which cleaves phosphodiester bonds at the 5' end of oligonucleotides, and a phospholipase, which catalyzes production of lysophosphatidic acid (LPA) in extracellular fluids. LPA evokes growth factor-like responses including stimulation of cell proliferation and chemotaxis. This gene product stimulates the motility of tumor cells and has angiogenic properties, and its expression is upregulated in several kinds of carcinomas. The gene product is secreted and further processed to make the biologically active form. Several alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040092.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENPP2	NM_001040092.3	MANE Select	c.1917+74A>G		intron	N/A	NP_001035181.1	Q13822-1
	ENPP2	NM_006209.5		c.2073+74A>G		intron	N/A	NP_006200.3
	ENPP2	NM_001130863.3		c.1992+74A>G		intron	N/A	NP_001124335.1	Q13822-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENPP2	ENST00000075322.11	TSL:1 MANE Select	c.1917+74A>G		intron	N/A	ENSP00000075322.6	Q13822-1
	ENPP2	ENST00000259486.10	TSL:1	c.2073+74A>G		intron	N/A	ENSP00000259486.6	Q13822-2
	ENPP2	ENST00000522826.5	TSL:1	c.1992+74A>G		intron	N/A	ENSP00000428291.1	Q13822-3

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17838 AN: 152100 Hom.: 1179 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0515

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0841

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.115 AC: 71996 AN: 625330 Hom.: 4603 AF XY: 0.117 AC XY: 38081 AN XY: 325272

African (AFR) AF: 0.147 AC: 1797 AN: 12188

American (AMR) AF: 0.0687 AC: 764 AN: 11120

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 2402 AN: 16868

East Asian (EAS) AF: 0.0412 AC: 1072 AN: 26010

South Asian (SAS) AF: 0.158 AC: 6638 AN: 42000

European-Finnish (FIN) AF: 0.0953 AC: 4317 AN: 45300

Middle Eastern (MID) AF: 0.0970 AC: 268 AN: 2762

European-Non Finnish (NFE) AF: 0.117 AC: 51102 AN: 438152

Other (OTH) AF: 0.118 AC: 3636 AN: 30930

GnomAD4 genome AF: 0.117 AC: 17852 AN: 152218 Hom.: 1182 Cov.: 32 AF XY: 0.116 AC XY: 8622 AN XY: 74428

African (AFR) AF: 0.144 AC: 5970 AN: 41534

American (AMR) AF: 0.0834 AC: 1275 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3472

East Asian (EAS) AF: 0.0514 AC: 267 AN: 5192

South Asian (SAS) AF: 0.166 AC: 799 AN: 4818

European-Finnish (FIN) AF: 0.0841 AC: 891 AN: 10600

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7787 AN: 68006

Other (OTH) AF: 0.112 AC: 237 AN: 2112

Alfa AF: 0.113 Hom.: 1157

Bravo AF: 0.116

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.61
DANN	Benign	0.78
PhyloP100		-1.6
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: rs16892786; hg19: chr8-120582871;