17-79733617-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_178543.5(ENPP7):c.363C>T(p.Asn121Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,612,942 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
Consequence
NM_178543.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ENPP7 | NM_178543.5 | c.363C>T | p.Asn121Asn | synonymous_variant | Exon 2 of 6 | ENST00000328313.10 | NP_848638.3 | |
ENPP7 | XM_011524737.2 | c.456C>T | p.Asn152Asn | synonymous_variant | Exon 2 of 5 | XP_011523039.2 | ||
ENPP7 | XR_001752505.2 | n.560C>T | non_coding_transcript_exon_variant | Exon 2 of 5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000840 AC: 21AN: 250130Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135484
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1460684Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 726660
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74394
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at