rs7768480
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006208.3(ENPP1):c.2101-53A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,532,622 control chromosomes in the GnomAD database, including 15,259 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.21 ( 5428 hom., cov: 31)
Exomes 𝑓: 0.097 ( 9831 hom. )
Consequence
ENPP1
NM_006208.3 intron
NM_006208.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.46
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 6-131882292-A-G is Benign according to our data. Variant chr6-131882292-A-G is described in ClinVar as [Benign]. Clinvar id is 1230336.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENPP1 | NM_006208.3 | c.2101-53A>G | intron_variant | ENST00000647893.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENPP1 | ENST00000647893.1 | c.2101-53A>G | intron_variant | NM_006208.3 | P1 | ||||
ENPP1 | ENST00000513998.5 | c.*938-53A>G | intron_variant, NMD_transcript_variant | 5 | |||||
ENPP1 | ENST00000684674.1 | n.532-53A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.205 AC: 30819AN: 150416Hom.: 5415 Cov.: 31
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GnomAD4 exome AF: 0.0971 AC: 134182AN: 1382102Hom.: 9831 AF XY: 0.0963 AC XY: 66623AN XY: 691742
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GnomAD4 genome ? AF: 0.205 AC: 30873AN: 150520Hom.: 5428 Cov.: 31 AF XY: 0.201 AC XY: 14764AN XY: 73508
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at