rs1409184

Variant names:

• chr6-131819351-G-A
• rs1409184
• NM_006208.3:c.240+11076G>A

Variant summary

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

The NM_006208.3(ENPP1):​c.240+11076G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,006 control chromosomes in the GnomAD database, including 10,163 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 (10163 hom., cov: 33)
• Consequence: ENPP1 NM_006208.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 5 publications found

Genes affected

ENPP1 (HGNC:3356): (ectonucleotide pyrophosphatase/phosphodiesterase 1) This gene is a member of the ecto-nucleotide pyrophosphatase/phosphodiesterase (ENPP) family. The encoded protein is a type II transmembrane glycoprotein comprising two identical disulfide-bonded subunits. This protein has broad specificity and cleaves a variety of substrates, including phosphodiester bonds of nucleotides and nucleotide sugars and pyrophosphate bonds of nucleotides and nucleotide sugars. This protein may function to hydrolyze nucleoside 5' triphosphates to their corresponding monophosphates and may also hydrolyze diadenosine polyphosphates. Mutations in this gene have been associated with 'idiopathic' infantile arterial calcification, ossification of the posterior longitudinal ligament of the spine (OPLL), and insulin resistance. [provided by RefSeq, Jul 2008]

SELENOKP2 (HGNC:53725): (selenoprotein K pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006208.3. 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
	ENPP1	NM_006208.3	MANE Select	c.240+11076G>A		intron	N/A	NP_006199.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENPP1	ENST00000647893.1	MANE Select	c.240+11076G>A		intron	N/A	ENSP00000498074.1
	ENPP1	ENST00000486853.1	TSL:2	n.260+11076G>A		intron	N/A
	ENPP1	ENST00000513998.5	TSL:5	n.240+11076G>A		intron	N/A	ENSP00000422424.1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53759 AN: 151888 Hom.: 10163 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.354 AC: 53765 AN: 152006 Hom.: 10163 Cov.: 33 AF XY: 0.350 AC XY: 25969 AN XY: 74282

African (AFR) AF: 0.227 AC: 9423 AN: 41452

American (AMR) AF: 0.337 AC: 5154 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1437 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2350 AN: 5178

South Asian (SAS) AF: 0.358 AC: 1720 AN: 4808

European-Finnish (FIN) AF: 0.343 AC: 3610 AN: 10516

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28973 AN: 67974

Other (OTH) AF: 0.379 AC: 802 AN: 2114

Alfa AF: 0.407 Hom.: 6765

Bravo AF: 0.344

Asia WGS AF: 0.413 AC: 1430 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.71
PhyloP100		0.20
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: rs1409184; hg19: chr6-132140491;