NM_001012301.4:c.852C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B.
The NM_001012301.4(ARSI):c.852C>T(p.Tyr284Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00084 in 1,613,144 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00080 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00084 ( 2 hom. )
Consequence
ARSI
NM_001012301.4 synonymous
NM_001012301.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.17
Publications
0 publications found
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]
ARSI Gene-Disease associations (from GenCC):
- autosomal recessive spastic paraplegia type 66Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 5-150298072-G-A is Benign according to our data. Variant chr5-150298072-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 465197.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.17 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARSI | ENST00000328668.8 | c.852C>T | p.Tyr284Tyr | synonymous_variant | Exon 2 of 2 | 1 | NM_001012301.4 | ENSP00000333395.7 | ||
ARSI | ENST00000515301.2 | c.423C>T | p.Tyr141Tyr | synonymous_variant | Exon 2 of 2 | 4 | ENSP00000426879.2 | |||
ARSI | ENST00000509146.1 | c.*163C>T | downstream_gene_variant | 4 | ENSP00000420955.1 |
Frequencies
GnomAD3 genomes AF: 0.000803 AC: 122AN: 152004Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
122
AN:
152004
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:
GnomAD2 exomes AF: 0.000749 AC: 187AN: 249676 AF XY: 0.000791 show subpopulations
GnomAD2 exomes
AF:
AC:
187
AN:
249676
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000844 AC: 1233AN: 1461022Hom.: 2 Cov.: 30 AF XY: 0.000821 AC XY: 597AN XY: 726828 show subpopulations
GnomAD4 exome
AF:
AC:
1233
AN:
1461022
Hom.:
Cov.:
30
AF XY:
AC XY:
597
AN XY:
726828
show subpopulations
African (AFR)
AF:
AC:
6
AN:
33478
American (AMR)
AF:
AC:
20
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
102
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39698
South Asian (SAS)
AF:
AC:
3
AN:
86252
European-Finnish (FIN)
AF:
AC:
3
AN:
52572
Middle Eastern (MID)
AF:
AC:
1
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
1056
AN:
1112004
Other (OTH)
AF:
AC:
42
AN:
60390
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.480
Heterozygous variant carriers
0
84
168
253
337
421
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
42
84
126
168
210
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.000802 AC: 122AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.000820 AC XY: 61AN XY: 74354 show subpopulations
GnomAD4 genome
AF:
AC:
122
AN:
152122
Hom.:
Cov.:
32
AF XY:
AC XY:
61
AN XY:
74354
show subpopulations
African (AFR)
AF:
AC:
9
AN:
41486
American (AMR)
AF:
AC:
14
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
12
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5156
South Asian (SAS)
AF:
AC:
0
AN:
4816
European-Finnish (FIN)
AF:
AC:
0
AN:
10588
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
86
AN:
68006
Other (OTH)
AF:
AC:
1
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
5
10
16
21
26
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Jun 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
ARSI: BP4, BP7 -
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Spastic paraplegia Benign:1
Dec 04, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.