chr6-46168121-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001290072.2(ENPP5):āc.142A>Gā(p.Thr48Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000713 in 1,613,834 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T48M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001290072.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENPP5 | NM_001290072.2 | c.142A>G | p.Thr48Ala | missense_variant | 3/5 | ENST00000371383.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENPP5 | ENST00000371383.7 | c.142A>G | p.Thr48Ala | missense_variant | 3/5 | 1 | NM_001290072.2 | P1 | |
ENPP5 | ENST00000230565.3 | c.142A>G | p.Thr48Ala | missense_variant | 2/4 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250948Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135800
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461660Hom.: 1 Cov.: 36 AF XY: 0.0000688 AC XY: 50AN XY: 727102
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2023 | The c.142A>G (p.T48A) alteration is located in exon 2 (coding exon 1) of the ENPP5 gene. This alteration results from a A to G substitution at nucleotide position 142, causing the threonine (T) at amino acid position 48 to be replaced by an alanine (A). 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