rs1329159364
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3
The NM_000263.4(NAGLU):c.208G>C(p.Gly70Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 1,214,376 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. G70G) has been classified as Likely benign.
Frequency
Consequence
NM_000263.4 missense
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 |
---|---|---|---|---|---|---|---|
NAGLU | NM_000263.4 | c.208G>C | p.Gly70Arg | missense_variant | 1/6 | ENST00000225927.7 | |
NAGLU | XM_024450771.2 | c.208G>C | p.Gly70Arg | missense_variant | 1/7 | ||
NAGLU | XM_047436138.1 | c.-254G>C | 5_prime_UTR_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAGLU | ENST00000225927.7 | c.208G>C | p.Gly70Arg | missense_variant | 1/6 | 1 | NM_000263.4 | P1 | |
NAGLU | ENST00000586516.5 | upstream_gene_variant | 2 | ||||||
NAGLU | ENST00000591587.1 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000133 AC: 2AN: 149992Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000132 AC: 14AN: 1064384Hom.: 0 Cov.: 30 AF XY: 0.0000137 AC XY: 7AN XY: 510232
GnomAD4 genome ? AF: 0.0000133 AC: 2AN: 149992Hom.: 0 Cov.: 33 AF XY: 0.0000137 AC XY: 1AN XY: 73144
ClinVar
Submissions by phenotype
Mucopolysaccharidosis, MPS-III-B Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Apr 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at