rs200012526
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001012301.4(ARSI):c.87C>T(p.Ala29=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00439 in 1,604,888 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0035 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0045 ( 22 hom. )
Consequence
ARSI
NM_001012301.4 synonymous
NM_001012301.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.931
Genes affected
ARSI (HGNC:32521): (arylsulfatase family member I) This gene encodes a protein that belongs to a large family of sulfatases that hydrolyze sulfate esters and sulfamates. Members of this family play a role in several cellular processes, including hormone synthesis, cell signaling in development and degradation of macromolecules. The protein encoded by this gene is thought to be secreted, and to function in extracellular space. [provided by RefSeq, Jul 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
Variant 5-150302287-G-A is Benign according to our data. Variant chr5-150302287-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 465198.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.931 with no splicing effect.
BS2
?
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARSI | NM_001012301.4 | c.87C>T | p.Ala29= | synonymous_variant | 1/2 | ENST00000328668.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARSI | ENST00000328668.8 | c.87C>T | p.Ala29= | synonymous_variant | 1/2 | 1 | NM_001012301.4 | P1 | |
ARSI | ENST00000509146.1 | c.-118-3675C>T | intron_variant | 4 | |||||
ARSI | ENST00000515301.2 | c.-118-3675C>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00355 AC: 540AN: 152142Hom.: 3 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
540
AN:
152142
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00334 AC: 753AN: 225664Hom.: 2 AF XY: 0.00326 AC XY: 402AN XY: 123364
GnomAD3 exomes
AF:
AC:
753
AN:
225664
Hom.:
AF XY:
AC XY:
402
AN XY:
123364
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00448 AC: 6508AN: 1452630Hom.: 22 Cov.: 31 AF XY: 0.00436 AC XY: 3145AN XY: 722044
GnomAD4 exome
AF:
AC:
6508
AN:
1452630
Hom.:
Cov.:
31
AF XY:
AC XY:
3145
AN XY:
722044
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00355 AC: 540AN: 152258Hom.: 3 Cov.: 32 AF XY: 0.00325 AC XY: 242AN XY: 74428
GnomAD4 genome
?
AF:
AC:
540
AN:
152258
Hom.:
Cov.:
32
AF XY:
AC XY:
242
AN XY:
74428
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | ARSI: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at