rs11752816
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014936.5(ENPP4):c.-9G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,345,790 control chromosomes in the GnomAD database, including 20,705 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 0.13 ( 1793 hom., cov: 31)
Exomes 𝑓: 0.17 ( 18912 hom. )
Consequence
ENPP4
NM_014936.5 5_prime_UTR
NM_014936.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.146
Genes affected
ENPP4 (HGNC:3359): (ectonucleotide pyrophosphatase/phosphodiesterase 4) Enables bis(5'-adenosyl)-triphosphatase activity. Involved in positive regulation of blood coagulation and purine ribonucleoside catabolic process. Located in extracellular exosome and membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.77).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENPP4 | NM_014936.5 | c.-9G>A | 5_prime_UTR_variant | 2/4 | ENST00000321037.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENPP4 | ENST00000321037.5 | c.-9G>A | 5_prime_UTR_variant | 2/4 | 1 | NM_014936.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.133 AC: 20096AN: 151322Hom.: 1793 Cov.: 31
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GnomAD3 exomes AF: 0.173 AC: 42264AN: 244884Hom.: 4467 AF XY: 0.182 AC XY: 24138AN XY: 132308
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GnomAD4 exome AF: 0.168 AC: 200327AN: 1194348Hom.: 18912 Cov.: 16 AF XY: 0.174 AC XY: 105463AN XY: 607622
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GnomAD4 genome ? AF: 0.133 AC: 20097AN: 151442Hom.: 1793 Cov.: 31 AF XY: 0.136 AC XY: 10083AN XY: 73986
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at