chr22:50625988:T>C Detail (hg38) (ARSA)

Information

Genome

Assembly Position
hg19 chr22:51,064,416-51,064,416 View the variant detail on this assembly version.
hg38 chr22:50,625,988-50,625,988

HGVS

Type Transcript Protein
RefSeq NM_000487.5:c.1055A>G NP_000478.3:p.Asn352Ser
NM_001085426.2:c.1055A>G NP_001078895.2:p.Asn352Ser
NM_001085427.2:c.1055A>G NP_001078896.2:p.Asn352Ser
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.153
ToMMo:0.158
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.228

Prediction

ClinVar

Clinical Significance Benign Likely benign; other
Review star
Show details
Links
Type Database ID Link
Gene MIM 607574 OMIM
HGNC 713 HGNC
Ensembl ENSG00000100299 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv66342979 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 1997-12-01 no assertion criteria provided ARYLSULFATASE A POLYMORPHISM germline Detail
Benign Likely benign 2024-02-01 criteria provided, multiple submitters, no conflicts metachromatic leukodystrophy germline not applicable unknown Detail
Benign; other 2021-11-11 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign criteria provided, single submitter not specified germline Detail
Uncertain significance no assertion criteria provided Metachromatic leukodystrophy, juvenile type unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.514 Leukodystrophy, Metachromatic NA CLINVAR Detail
0.514 Leukodystrophy, Metachromatic In addition, the presence of the most common mutations associated with ASA pseud... BeFree 16613739 Detail
0.124 Metachromatic Leukodystrophy, Infant A late infantile metachromatic leukodystrophy patient was found to be heterozygo... BeFree 14571263 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000487.6(ARSA):c.1055A>G (p.Asn352Ser) AND ARYLSULFATASE A POLYMORPHISM ClinVar Detail
NM_000487.6(ARSA):c.1055A>G (p.Asn352Ser) AND Metachromatic leukodystrophy ClinVar Detail
NM_000487.6(ARSA):c.1055A>G (p.Asn352Ser) AND not provided ClinVar Detail
NM_000487.6(ARSA):c.1055A>G (p.Asn352Ser) AND not specified ClinVar Detail
NM_000487.6(ARSA):c.1055A>G (p.Asn352Ser) AND Metachromatic leukodystrophy, juvenile type ClinVar Detail
NA DisGeNET Detail
In addition, the presence of the most common mutations associated with ASA pseudo-deficiency (N350S,... DisGeNET Detail
A late infantile metachromatic leukodystrophy patient was found to be heterozygous for the arylsulfa... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2071421 dbSNP
Genome
hg38
Position
chr22:50,625,988-50,625,988
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1026
Mean of sample read depth (HGVD)
25.39
Standard deviation of sample read depth (HGVD)
11.54
Number of reference allele (HGVD)
1739
Number of alternative allele (HGVD)
313
Allele Frequency (HGVD)
0.15253411306042886
Gene Symbol (HGVD)
ARSA
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs2071421
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.158
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2648
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
3318
East Asian Allele Counts (ExAC)
758
East Asian Heterozygous Counts (ExAC)
618
East Asian Homozygous Counts (ExAC)
70
East Asian Allele Frequency (ExAC)
0.22845087402049427
Chromosome Counts in All Race (ExAC)
40070
Allele Counts in All Race (ExAC)
8679
Heterozygous Counts in All Race (ExAC)
7001
Homozygous Counts in All Race (ExAC)
839
Allele Frequency in All Race (ExAC)
0.21659595707511856
Genome browser