chr16-1352142-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_StrongBS1
The NM_032520.5(GNPTG):āc.93G>Cā(p.Glu31Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000169 in 1,581,940 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E31K) has been classified as Uncertain significance.
Frequency
Consequence
NM_032520.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNPTG | NM_032520.5 | c.93G>C | p.Glu31Asp | missense_variant | 2/11 | ENST00000204679.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPTG | ENST00000204679.9 | c.93G>C | p.Glu31Asp | missense_variant | 2/11 | 1 | NM_032520.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000946 AC: 144AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000151 AC: 29AN: 192460Hom.: 0 AF XY: 0.000124 AC XY: 13AN XY: 104900
GnomAD4 exome AF: 0.0000867 AC: 124AN: 1429626Hom.: 0 Cov.: 32 AF XY: 0.0000889 AC XY: 63AN XY: 708328
GnomAD4 genome AF: 0.000945 AC: 144AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000980 AC XY: 73AN XY: 74490
ClinVar
Submissions by phenotype
GNPTG-mucolipidosis Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Jan 19, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at