chr6-131808140-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_006208.3(ENPP1):c.105C>T(p.His35=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000235 in 1,403,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000027 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
ENPP1
NM_006208.3 synonymous
NM_006208.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.205
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
?
Variant 6-131808140-C-T is Benign according to our data. Variant chr6-131808140-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2897393.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.205 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENPP1 | NM_006208.3 | c.105C>T | p.His35= | synonymous_variant | 1/25 | ENST00000647893.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENPP1 | ENST00000647893.1 | c.105C>T | p.His35= | synonymous_variant | 1/25 | NM_006208.3 | P1 | ||
ENPP1 | ENST00000486853.1 | n.125C>T | non_coding_transcript_exon_variant | 1/4 | 2 | ||||
ENPP1 | ENST00000513998.5 | c.105C>T | p.His35= | synonymous_variant, NMD_transcript_variant | 1/25 | 5 | |||
ENPP1 | ENST00000650507.1 | c.18C>T | p.His6= | synonymous_variant, NMD_transcript_variant | 1/4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000266 AC: 4AN: 150508Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000231 AC: 29AN: 1253474Hom.: 0 Cov.: 33 AF XY: 0.0000131 AC XY: 8AN XY: 611618
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GnomAD4 genome ? AF: 0.0000266 AC: 4AN: 150508Hom.: 0 Cov.: 32 AF XY: 0.0000408 AC XY: 3AN XY: 73460
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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 | Invitae | Mar 08, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at