6-131847856-GGTGTGTGTGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGTGT
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_006208.3(ENPP1):c.313+45_313+46delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,151,148 control chromosomes in the GnomAD database, including 1,863 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.14 ( 1306 hom., cov: 0)
Exomes 𝑓: 0.15 ( 557 hom. )
Consequence
ENPP1
NM_006208.3 intron
NM_006208.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.525
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 6-131847856-GGT-G is Benign according to our data. Variant chr6-131847856-GGT-G is described in ClinVar as [Benign]. Clinvar id is 355332.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-131847856-GGT-G is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENPP1 | ENST00000647893.1 | c.313+9_313+10delGT | intron_variant | NM_006208.3 | ENSP00000498074.1 | |||||
ENPP1 | ENST00000486853.1 | n.333+9_333+10delGT | intron_variant | 2 | ||||||
ENPP1 | ENST00000513998.5 | n.313+9_313+10delGT | intron_variant | 5 | ENSP00000422424.1 | |||||
ENPP1 | ENST00000650507.1 | n.*149+9_*149+10delGT | intron_variant | ENSP00000497375.1 |
Frequencies
GnomAD3 genomes AF: 0.143 AC: 19621AN: 136864Hom.: 1307 Cov.: 0
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GnomAD4 exome AF: 0.154 AC: 155702AN: 1014198Hom.: 557 AF XY: 0.160 AC XY: 81912AN XY: 513220
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GnomAD4 genome AF: 0.143 AC: 19625AN: 136950Hom.: 1306 Cov.: 0 AF XY: 0.150 AC XY: 9982AN XY: 66570
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 20, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Hypophosphatemic Rickets, Recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Arterial calcification, generalized, of infancy, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at