rs453639
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005021.5(ENPP3):c.1953+2317C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,088 control chromosomes in the GnomAD database, including 44,618 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.75 ( 44618 hom., cov: 32)
Consequence
ENPP3
NM_005021.5 intron
NM_005021.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.63
Genes affected
ENPP3 (HGNC:3358): (ectonucleotide pyrophosphatase/phosphodiesterase 3) The protein encoded by this gene belongs to a series of ectoenzymes that are involved in hydrolysis of extracellular nucleotides. These ectoenzymes possess ATPase and ATP pyrophosphatase activities and are type II transmembrane proteins. Expression of the related rat mRNA has been found in a subset of immature glial cells and in the alimentary tract. The corresponding rat protein has been detected in the pancreas, small intestine, colon, and liver. The human mRNA is expressed in glioma cells, prostate, and uterus. Expression of the human protein has been detected in uterus, basophils, and mast cells. Two transcript variants, one protein coding and the other non-protein coding, have been found for this gene. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENPP3 | NM_005021.5 | c.1953+2317C>A | intron_variant | ENST00000357639.8 | |||
ENPP3 | XM_011535897.2 | c.1191+2317C>A | intron_variant | ||||
ENPP3 | XM_017010932.2 | c.1722+2317C>A | intron_variant | ||||
ENPP3 | NR_133007.2 | n.2036+2317C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENPP3 | ENST00000357639.8 | c.1953+2317C>A | intron_variant | 1 | NM_005021.5 | P1 | |||
ENPP3 | ENST00000358229.6 | c.1953+2317C>A | intron_variant | 1 | |||||
ENPP3 | ENST00000414305.5 | c.1953+2317C>A | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.754 AC: 114565AN: 151970Hom.: 44549 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.754 AC: 114694AN: 152088Hom.: 44618 Cov.: 32 AF XY: 0.758 AC XY: 56334AN XY: 74340
GnomAD4 genome
?
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114694
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32
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56334
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3068
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at