22-42061040-G-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_000262.3(NAGA):c.985C>A(p.Arg329=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000262.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAGA | NM_000262.3 | c.985C>A | p.Arg329= | synonymous_variant | 8/9 | ENST00000396398.8 | |
NAGA | NM_001362848.1 | c.985C>A | p.Arg329= | synonymous_variant | 9/10 | ||
NAGA | NM_001362850.1 | c.985C>A | p.Arg329= | synonymous_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAGA | ENST00000396398.8 | c.985C>A | p.Arg329= | synonymous_variant | 8/9 | 1 | NM_000262.3 | P1 | |
NAGA | ENST00000402937.1 | c.985C>A | p.Arg329= | synonymous_variant | 9/10 | 5 | P1 | ||
NAGA | ENST00000403363.5 | c.985C>A | p.Arg329= | synonymous_variant | 9/10 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461832Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727224
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at