rs200182983
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000487.6(ARSA):c.636C>T(p.Ala212=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000446 in 1,613,512 control chromosomes in the GnomAD database, including 9 homozygotes. 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. A212A) has been classified as Likely benign.
Frequency
Consequence
NM_000487.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARSA | NM_000487.6 | c.636C>T | p.Ala212= | synonymous_variant | 3/8 | ENST00000216124.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARSA | ENST00000216124.10 | c.636C>T | p.Ala212= | synonymous_variant | 3/8 | 1 | NM_000487.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000296 AC: 45AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000726 AC: 182AN: 250676Hom.: 0 AF XY: 0.000973 AC XY: 132AN XY: 135692
GnomAD4 exome AF: 0.000461 AC: 674AN: 1461142Hom.: 9 Cov.: 33 AF XY: 0.000596 AC XY: 433AN XY: 726846
GnomAD4 genome AF: 0.000295 AC: 45AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.000362 AC XY: 27AN XY: 74504
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 26, 2012 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | ARSA: BP4, BP7 - |
Metachromatic leukodystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at