rs780527821
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000263.4(NAGLU):c.1621C>A(p.Arg541=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,460,698 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R541R) has been classified as Likely benign.
Frequency
Consequence
NM_000263.4 synonymous
Scores
Clinical Significance
Conservation
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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.1621C>A | p.Arg541= | synonymous_variant | 6/6 | ENST00000225927.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAGLU | ENST00000225927.7 | c.1621C>A | p.Arg541= | synonymous_variant | 6/6 | 1 | NM_000263.4 | P1 | |
NAGLU | ENST00000591587.1 | c.*590C>A | 3_prime_UTR_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247170Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134542
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460698Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 726660
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Mucopolysaccharidosis, MPS-III-B;C5569050:Charcot-Marie-Tooth disease axonal type 2V Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at