chr6-131860504-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM5PP3
The NM_006208.3(ENPP1):c.913C>T(p.Pro305Ser) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000189 in 1,589,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P305T) has been classified as Pathogenic.
Frequency
Consequence
NM_006208.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENPP1 | NM_006208.3 | c.913C>T | p.Pro305Ser | missense_variant, splice_region_variant | 8/25 | ENST00000647893.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENPP1 | ENST00000647893.1 | c.913C>T | p.Pro305Ser | missense_variant, splice_region_variant | 8/25 | NM_006208.3 | P1 | ||
ENPP1 | ENST00000513998.5 | c.913C>T | p.Pro305Ser | missense_variant, splice_region_variant, NMD_transcript_variant | 8/25 | 5 | |||
ENPP1 | ENST00000650147.1 | c.*198C>T | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 5/7 | |||||
ENPP1 | ENST00000650437.1 | c.*198C>T | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 4/14 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1436958Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 716492
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74264
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at