rs659497
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_000263.4(NAGLU):c.423T>A(p.Ser141=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S141S) has been classified as Benign.
Frequency
Consequence
NM_000263.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAGLU | NM_000263.4 | c.423T>A | p.Ser141= | synonymous_variant | 2/6 | ENST00000225927.7 | |
NAGLU | XM_024450771.2 | c.480T>A | p.Ser160= | synonymous_variant | 3/7 | ||
NAGLU | XM_047436138.1 | c.-79+782T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAGLU | ENST00000225927.7 | c.423T>A | p.Ser141= | synonymous_variant | 2/6 | 1 | NM_000263.4 | P1 | |
NAGLU | ENST00000590358.1 | c.111T>A | p.Ser37= | synonymous_variant | 1/2 | 4 | |||
NAGLU | ENST00000586516.5 | c.133+782T>A | intron_variant | 2 | |||||
NAGLU | ENST00000591587.1 | c.126+782T>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152254Hom.: 0 Cov.: 35 FAILED QC
GnomAD4 exome Cov.: 75
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152254Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 74388
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at