chr5-78985003-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_000046.5(ARSB):c.246G>A(p.Leu82=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000175 in 1,539,358 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L82L) has been classified as Likely benign.
Frequency
Consequence
NM_000046.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARSB | NM_000046.5 | c.246G>A | p.Leu82= | synonymous_variant | 1/8 | ENST00000264914.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARSB | ENST00000264914.10 | c.246G>A | p.Leu82= | synonymous_variant | 1/8 | 1 | NM_000046.5 | P1 | |
ARSB | ENST00000396151.7 | c.246G>A | p.Leu82= | synonymous_variant | 2/8 | 1 | |||
ARSB | ENST00000565165.2 | c.246G>A | p.Leu82= | synonymous_variant | 1/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151768Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000397 AC: 7AN: 176244Hom.: 0 AF XY: 0.0000500 AC XY: 5AN XY: 99946
GnomAD4 exome AF: 0.0000173 AC: 24AN: 1387590Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 18AN XY: 689762
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151768Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74152
ClinVar
Submissions by phenotype
Mucopolysaccharidosis type 6 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 25, 2023 | - - |
Uncertain significance, criteria provided, single submitter | curation | Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova | Jan 01, 2018 | Very low frequence in GnomAd (PM2) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at