Variant 6-131847856-GGTGTGTGTGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The NM_006208.3(ENPP1):c.313+39_313+46del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000459 in 1,181,894 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00044 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00046 ( 0 hom. )

Consequence

ENPP1
NM_006208.3 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.721

Variant links:

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]

ENPP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 6-131847856-GGTGTGTGT-G is Benign according to our data. Variant chr6-131847856-GGTGTGTGT-G is described in ClinVar as [Likely_benign]. Clinvar id is 1114458.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENPP1	NM_006208.3 linkuse as main transcript	c.313+39_313+46del		intron_variant		ENST00000647893.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
ENPP1	ENST00000647893.1 linkuse as main transcript	c.313+39_313+46del	intron_variant		NM_006208.3	P1
ENPP1	ENST00000513998.5 linkuse as main transcript	c.313+39_313+46del	intron_variant, NMD_transcript_variant	5
ENPP1	ENST00000650507.1 linkuse as main transcript	c.149+39_149+46del	intron_variant, NMD_transcript_variant
ENPP1	ENST00000486853.1 linkuse as main transcript	n.333+39_333+46del	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.000430

AC:

AN:

137174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00108

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000216

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000619

Gnomad SAS

AF:

0.000471

Gnomad FIN

AF:

0.000107

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000188

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000461

AC:

482

AN:

1044632

Hom.:

AF XY:

0.000393

AC XY:

208

AN XY:

529460

show subpopulations

Gnomad4 AFR exome

AF:

0.00480

Gnomad4 AMR exome

AF:

0.000336

Gnomad4 ASJ exome

AF:

0.0000989

Gnomad4 EAS exome

AF:

0.000280

Gnomad4 SAS exome

AF:

0.000255

Gnomad4 FIN exome

AF:

0.000101

Gnomad4 NFE exome

AF:

0.000386

Gnomad4 OTH exome

AF:

0.000529

GnomAD4 genome

AF:

0.000437

AC:

AN:

137262

Hom.:

Cov.:

AF XY:

0.000464

AC XY:

AN XY:

66774

show subpopulations

Gnomad4 AFR

AF:

0.00111

Gnomad4 AMR

AF:

0.000216

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000621

Gnomad4 SAS

AF:

0.000471

Gnomad4 FIN

AF:

0.000107

Gnomad4 NFE

AF:

0.000188

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 29, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over