17-79731153-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178543.5(ENPP7):c.14C>T(p.Ala5Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,456,240 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178543.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ENPP7 | NM_178543.5 | c.14C>T | p.Ala5Val | missense_variant | Exon 1 of 6 | ENST00000328313.10 | NP_848638.3 | |
ENPP7 | XM_011524737.2 | c.107C>T | p.Ala36Val | missense_variant | Exon 1 of 5 | XP_011523039.2 | ||
ENPP7 | XR_001752505.2 | n.211C>T | non_coding_transcript_exon_variant | Exon 1 of 5 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.0000125 AC: 3AN: 239928Hom.: 0 AF XY: 0.00000764 AC XY: 1AN XY: 130968
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1456240Hom.: 0 Cov.: 61 AF XY: 0.00000138 AC XY: 1AN XY: 724278
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.14C>T (p.A5V) alteration is located in exon 1 (coding exon 1) of the ENPP7 gene. This alteration results from a C to T substitution at nucleotide position 14, causing the alanine (A) at amino acid position 5 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at