6-131847856-GGTGTGTGTGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGTGTGTGT
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_006208.3(ENPP1):c.313+45_313+46dupGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.20 ( 2793 hom., cov: 0)
Exomes 𝑓: 0.12 ( 194 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 -9 ACMG points.
BP6
Variant 6-131847856-G-GGT is Benign according to our data. Variant chr6-131847856-G-GGT is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 355328.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=2, Benign=3}.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 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+8_313+9insGT | intron_variant | NM_006208.3 | ENSP00000498074.1 | |||||
ENPP1 | ENST00000486853.1 | n.333+8_333+9insGT | intron_variant | 2 | ||||||
ENPP1 | ENST00000513998.5 | n.313+8_313+9insGT | intron_variant | 5 | ENSP00000422424.1 | |||||
ENPP1 | ENST00000650507.1 | n.*149+8_*149+9insGT | intron_variant | ENSP00000497375.1 |
Frequencies
GnomAD3 genomes AF: 0.201 AC: 27476AN: 136968Hom.: 2795 Cov.: 0
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GnomAD4 exome AF: 0.116 AC: 120008AN: 1030852Hom.: 194 Cov.: 14 AF XY: 0.122 AC XY: 63581AN XY: 522134
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GnomAD4 genome AF: 0.200 AC: 27479AN: 137056Hom.: 2793 Cov.: 0 AF XY: 0.204 AC XY: 13633AN XY: 66670
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:5
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 09, 2019 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Hypophosphatemic Rickets, Recessive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Arterial calcification, generalized, of infancy, 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital | Jul 19, 2020 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at