chr16-1351962-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032520.5(GNPTG):c.-4C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000154 in 1,297,716 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 Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
GNPTG
NM_032520.5 5_prime_UTR
NM_032520.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.49
Genes affected
GNPTG (HGNC:23026): (N-acetylglucosamine-1-phosphate transferase subunit gamma) This gene encodes the gamma sunbunit of the N-acetylglucosamine-1-phosphotransferase complex. This hexameric complex, composed of alpha, beta and gamma subunits, catalyzes the first step in synthesis of a mannose 6-phosphate lysosomal recognition marker. This enzyme complex is necessary for targeting of lysosomal hydrolases to the lysosome. Mutations in the gene encoding the gamma subunit have been associated with mucolipidosis IIIC, also known as mucolipidosis III gamma.[provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNPTG | NM_032520.5 | c.-4C>T | 5_prime_UTR_variant | 1/11 | ENST00000204679.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPTG | ENST00000204679.9 | c.-4C>T | 5_prime_UTR_variant | 1/11 | 1 | NM_032520.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151626Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000648 AC: 1AN: 15438Hom.: 0 AF XY: 0.000101 AC XY: 1AN XY: 9880
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GnomAD4 exome AF: 0.0000131 AC: 15AN: 1145982Hom.: 0 Cov.: 32 AF XY: 0.0000181 AC XY: 10AN XY: 552778
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GnomAD4 genome AF: 0.0000330 AC: 5AN: 151734Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74162
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
GNPTG-mucolipidosis Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 24, 2020 | - - |
Computational scores
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Benign
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at