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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs74315464

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:50627048 (GRCh38.p13) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000008 (2/264690, TOPMED)
A=0.000007 (1/140284, GnomAD)
A=0.00000 (0/11862, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ARSA : Missense Variant
Publications
2 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p13 chr 22 NC_000022.11:g.50627048G>A
GRCh38.p13 chr 22 NC_000022.11:g.50627048G>C
GRCh37.p13 chr 22 NC_000022.10:g.51065476G>A
GRCh37.p13 chr 22 NC_000022.10:g.51065476G>C
ARSA RefSeqGene NG_009260.2:g.6132C>T
ARSA RefSeqGene NG_009260.2:g.6132C>G
Gene: ARSA, arylsulfatase A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ARSA transcript variant 1 NM_000487.6:c.470C>T P [CCC] > L [CTC] Coding Sequence Variant
arylsulfatase A isoform a precursor NP_000478.3:p.Pro157Leu P (Pro) > L (Leu) Missense Variant
ARSA transcript variant 1 NM_000487.6:c.470C>G P [CCC] > R [CGC] Coding Sequence Variant
arylsulfatase A isoform a precursor NP_000478.3:p.Pro157Arg P (Pro) > R (Arg) Missense Variant
ARSA transcript variant 5 NM_001085428.3:c.212C>T P [CCC] > L [CTC] Coding Sequence Variant
arylsulfatase A isoform b NP_001078897.1:p.Pro71Leu P (Pro) > L (Leu) Missense Variant
ARSA transcript variant 5 NM_001085428.3:c.212C>G P [CCC] > R [CGC] Coding Sequence Variant
arylsulfatase A isoform b NP_001078897.1:p.Pro71Arg P (Pro) > R (Arg) Missense Variant
ARSA transcript variant 6 NM_001362782.2:c.212C>T P [CCC] > L [CTC] Coding Sequence Variant
arylsulfatase A isoform b NP_001349711.1:p.Pro71Leu P (Pro) > L (Leu) Missense Variant
ARSA transcript variant 6 NM_001362782.2:c.212C>G P [CCC] > R [CGC] Coding Sequence Variant
arylsulfatase A isoform b NP_001349711.1:p.Pro71Arg P (Pro) > R (Arg) Missense Variant
ARSA transcript variant 2 NM_001085425.3:c.470C>T P [CCC] > L [CTC] Coding Sequence Variant
arylsulfatase A isoform a precursor NP_001078894.2:p.Pro157Leu P (Pro) > L (Leu) Missense Variant
ARSA transcript variant 2 NM_001085425.3:c.470C>G P [CCC] > R [CGC] Coding Sequence Variant
arylsulfatase A isoform a precursor NP_001078894.2:p.Pro157Arg P (Pro) > R (Arg) Missense Variant
ARSA transcript variant 3 NM_001085426.3:c.470C>T P [CCC] > L [CTC] Coding Sequence Variant
arylsulfatase A isoform a precursor NP_001078895.2:p.Pro157Leu P (Pro) > L (Leu) Missense Variant
ARSA transcript variant 3 NM_001085426.3:c.470C>G P [CCC] > R [CGC] Coding Sequence Variant
arylsulfatase A isoform a precursor NP_001078895.2:p.Pro157Arg P (Pro) > R (Arg) Missense Variant
ARSA transcript variant 4 NM_001085427.3:c.470C>T P [CCC] > L [CTC] Coding Sequence Variant
arylsulfatase A isoform a precursor NP_001078896.2:p.Pro157Leu P (Pro) > L (Leu) Missense Variant
ARSA transcript variant 4 NM_001085427.3:c.470C>G P [CCC] > R [CGC] Coding Sequence Variant
arylsulfatase A isoform a precursor NP_001078896.2:p.Pro157Arg P (Pro) > R (Arg) Missense Variant
ARSA transcript variant X1 XM_017028800.1:c.470C>T P [CCC] > L [CTC] Coding Sequence Variant
arylsulfatase A isoform X1 XP_016884289.1:p.Pro157Leu P (Pro) > L (Leu) Missense Variant
ARSA transcript variant X1 XM_017028800.1:c.470C>G P [CCC] > R [CGC] Coding Sequence Variant
arylsulfatase A isoform X1 XP_016884289.1:p.Pro157Arg P (Pro) > R (Arg) Missense Variant
ARSA transcript variant X3 XM_011530691.3:c.470C>T P [CCC] > L [CTC] Coding Sequence Variant
arylsulfatase A isoform X3 XP_011528993.1:p.Pro157Leu P (Pro) > L (Leu) Missense Variant
ARSA transcript variant X3 XM_011530691.3:c.470C>G P [CCC] > R [CGC] Coding Sequence Variant
arylsulfatase A isoform X3 XP_011528993.1:p.Pro157Arg P (Pro) > R (Arg) Missense Variant
ARSA transcript variant X4 XM_024452241.1:c.470C>T P [CCC] > L [CTC] Coding Sequence Variant
arylsulfatase A isoform X3 XP_024308009.1:p.Pro157Leu P (Pro) > L (Leu) Missense Variant
ARSA transcript variant X4 XM_024452241.1:c.470C>G P [CCC] > R [CGC] Coding Sequence Variant
arylsulfatase A isoform X3 XP_024308009.1:p.Pro157Arg P (Pro) > R (Arg) Missense Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: A (allele ID: 79028 )
ClinVar Accession Disease Names Clinical Significance
RCV000058968.1 not provided Not-Provided
RCV000778670.1 Metachromatic leukodystrophy Uncertain-Significance
Allele: C (allele ID: 18106 )
ClinVar Accession Disease Names Clinical Significance
RCV000003213.4 Arylsulfatase A pseudodeficiency Pathogenic

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 11862 G=1.00000 A=0.00000
European Sub 7618 G=1.0000 A=0.0000
African Sub 2816 G=1.0000 A=0.0000
African Others Sub 108 G=1.000 A=0.000
African American Sub 2708 G=1.0000 A=0.0000
Asian Sub 108 G=1.000 A=0.000
East Asian Sub 84 G=1.00 A=0.00
Other Asian Sub 24 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 94 G=1.00 A=0.00
Other Sub 470 G=1.000 A=0.000


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.999992 A=0.000008
gnomAD - Genomes Global Study-wide 140284 G=0.999993 A=0.000007
gnomAD - Genomes European Sub 75950 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42058 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13666 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement G= A C
GRCh38.p13 chr 22 NC_000022.11:g.50627048= NC_000022.11:g.50627048G>A NC_000022.11:g.50627048G>C
GRCh37.p13 chr 22 NC_000022.10:g.51065476= NC_000022.10:g.51065476G>A NC_000022.10:g.51065476G>C
ARSA RefSeqGene NG_009260.2:g.6132= NG_009260.2:g.6132C>T NG_009260.2:g.6132C>G
ARSA transcript variant 1 NM_000487.6:c.470= NM_000487.6:c.470C>T NM_000487.6:c.470C>G
ARSA transcript variant 1 NM_000487.5:c.470= NM_000487.5:c.470C>T NM_000487.5:c.470C>G
ARSA transcript variant 2 NM_001085425.3:c.470= NM_001085425.3:c.470C>T NM_001085425.3:c.470C>G
ARSA transcript variant 2 NM_001085425.2:c.470= NM_001085425.2:c.470C>T NM_001085425.2:c.470C>G
ARSA transcript variant 3 NM_001085426.3:c.470= NM_001085426.3:c.470C>T NM_001085426.3:c.470C>G
ARSA transcript variant 3 NM_001085426.2:c.470= NM_001085426.2:c.470C>T NM_001085426.2:c.470C>G
ARSA transcript variant 4 NM_001085427.3:c.470= NM_001085427.3:c.470C>T NM_001085427.3:c.470C>G
ARSA transcript variant 4 NM_001085427.2:c.470= NM_001085427.2:c.470C>T NM_001085427.2:c.470C>G
ARSA transcript variant 5 NM_001085428.3:c.212= NM_001085428.3:c.212C>T NM_001085428.3:c.212C>G
ARSA transcript variant 5 NM_001085428.2:c.212= NM_001085428.2:c.212C>T NM_001085428.2:c.212C>G
ARSA transcript variant 6 NM_001362782.2:c.212= NM_001362782.2:c.212C>T NM_001362782.2:c.212C>G
ARSA transcript variant 6 NM_001362782.1:c.212= NM_001362782.1:c.212C>T NM_001362782.1:c.212C>G
ARSA transcript variant X3 XM_011530691.3:c.470= XM_011530691.3:c.470C>T XM_011530691.3:c.470C>G
ARSA transcript variant X1 XM_017028800.1:c.470= XM_017028800.1:c.470C>T XM_017028800.1:c.470C>G
ARSA transcript variant X4 XM_024452241.1:c.470= XM_024452241.1:c.470C>T XM_024452241.1:c.470C>G
arylsulfatase A isoform a precursor NP_000478.3:p.Pro157= NP_000478.3:p.Pro157Leu NP_000478.3:p.Pro157Arg
arylsulfatase A isoform a precursor NP_001078894.2:p.Pro157= NP_001078894.2:p.Pro157Leu NP_001078894.2:p.Pro157Arg
arylsulfatase A isoform a precursor NP_001078895.2:p.Pro157= NP_001078895.2:p.Pro157Leu NP_001078895.2:p.Pro157Arg
arylsulfatase A isoform a precursor NP_001078896.2:p.Pro157= NP_001078896.2:p.Pro157Leu NP_001078896.2:p.Pro157Arg
arylsulfatase A isoform b NP_001078897.1:p.Pro71= NP_001078897.1:p.Pro71Leu NP_001078897.1:p.Pro71Arg
arylsulfatase A isoform b NP_001349711.1:p.Pro71= NP_001349711.1:p.Pro71Leu NP_001349711.1:p.Pro71Arg
arylsulfatase A isoform X3 XP_011528993.1:p.Pro157= XP_011528993.1:p.Pro157Leu XP_011528993.1:p.Pro157Arg
arylsulfatase A isoform X1 XP_016884289.1:p.Pro157= XP_016884289.1:p.Pro157Leu XP_016884289.1:p.Pro157Arg
arylsulfatase A isoform X3 XP_024308009.1:p.Pro157= XP_024308009.1:p.Pro157Leu XP_024308009.1:p.Pro157Arg
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

6 SubSNP, 3 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMICIA ss179320309 Aug 28, 2012 (137)
2 OMIM-CURATED-RECORDS ss256240182 Aug 23, 2010 (132)
3 SWISSPROT ss514155036 Apr 18, 2012 (136)
4 GNOMAD ss2750599564 Nov 08, 2017 (151)
5 GNOMAD ss2975722107 Nov 08, 2017 (151)
6 TOPMED ss5113235582 Apr 27, 2021 (155)
7 gnomAD - Genomes NC_000022.11 - 50627048 Apr 27, 2021 (155)
8 TopMed NC_000022.11 - 50627048 Apr 27, 2021 (155)
9 ALFA NC_000022.11 - 50627048 Apr 27, 2021 (155)
10 ClinVar RCV000003213.4 Jul 13, 2019 (153)
11 ClinVar RCV000058968.1 Oct 12, 2018 (152)
12 ClinVar RCV000778670.1 Jul 13, 2019 (153)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2750599564, ss2975722107 NC_000022.10:51065475:G:A NC_000022.11:50627047:G:A (self)
RCV000058968.1, RCV000778670.1, 573335300, 388344529, 10641027270, ss514155036, ss5113235582 NC_000022.11:50627047:G:A NC_000022.11:50627047:G:A (self)
RCV000003213.4, ss179320309, ss256240182 NC_000022.11:50627047:G:C NC_000022.11:50627047:G:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs74315464
PMID Title Author Year Journal
7866401 Molecular genetics of metachromatic leukodystrophy. Gieselmann V et al. 1994 Human mutation
14517960 Identification of nine novel arylsulfatase a (ARSA) gene mutations in patients with metachromatic leukodystrophy (MLD). Eng B et al. 2003 Human mutation
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post596+ae089ad