Name: rs1489735173
Published: September 21, 2022
License: Open Access

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.

rs1489735173

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:68280200-68280202 (GRCh38.p14) 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: delGA
Variation Type: Indel Insertion and Deletion
Frequency: delGA=0.000160 (22/137084, GnomAD)
delGA=0.00025 (3/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ARSG : Intron Variant
SLC16A6 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	HTRZ	HWEP
Total	Global	11862	AGA=0.99975	A=0.00025	0.999494	0.000506	0
European	Sub	7618	AGA=1.0000	A=0.0000	1.0	0.0	N/A
African	Sub	2816	AGA=0.9989	A=0.0011	0.997869	0.002131	0
African Others	Sub	108	AGA=1.000	A=0.000	1.0	0.0	N/A
African American	Sub	2708	AGA=0.9989	A=0.0011	0.997784	0.002216	0
Asian	Sub	108	AGA=1.000	A=0.000	1.0	0.0	N/A
East Asian	Sub	84	AGA=1.00	A=0.00	1.0	0.0	N/A
Other Asian	Sub	24	AGA=1.00	A=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	AGA=1.000	A=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	AGA=1.000	A=0.000	1.0	0.0	N/A
South Asian	Sub	94	AGA=1.00	A=0.00	1.0	0.0	N/A
Other	Sub	470	AGA=1.000	A=0.000	1.0	0.0	N/A

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Genomes	Global	Study-wide	137084	AGA=0.999840	delGA=0.000160
gnomAD - Genomes	European	Sub	74636	AGA=0.99997	delGA=0.00003
gnomAD - Genomes	African	Sub	40544	AGA=0.99958	delGA=0.00042
gnomAD - Genomes	American	Sub	13370	AGA=0.99993	delGA=0.00007
gnomAD - Genomes	Ashkenazi Jewish	Sub	3304	AGA=1.0000	delGA=0.0000
gnomAD - Genomes	East Asian	Sub	3110	AGA=1.0000	delGA=0.0000
gnomAD - Genomes	Other	Sub	2120	AGA=0.9991	delGA=0.0009
Allele Frequency Aggregator	Total	Global	11862	AGA=0.99975	delGA=0.00025
Allele Frequency Aggregator	European	Sub	7618	AGA=1.0000	delGA=0.0000
Allele Frequency Aggregator	African	Sub	2816	AGA=0.9989	delGA=0.0011
Allele Frequency Aggregator	Latin American 2	Sub	610	AGA=1.000	delGA=0.000
Allele Frequency Aggregator	Other	Sub	470	AGA=1.000	delGA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	AGA=1.000	delGA=0.000
Allele Frequency Aggregator	Asian	Sub	108	AGA=1.000	delGA=0.000
Allele Frequency Aggregator	South Asian	Sub	94	AGA=1.00	delGA=0.00

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.p14 chr 17	NC_000017.11:g.68280201_68280202del
GRCh37.p13 chr 17	NC_000017.10:g.66276342_66276343del
ARSG RefSeqGene	NG_032814.2:g.26113_26114del
GRCh37.p13 chr 17 fix patch HG747_PATCH	NW_003871088.1:g.340212_340213del

Gene: SLC16A6, solute carrier family 16 member 6 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC16A6 transcript variant 1	NM_001174166.2:c.-7-1874_… NM_001174166.2:c.-7-1874_-7-1873del	N/A	Intron Variant
SLC16A6 transcript variant 2	NM_004694.5:c.-7-1874_-7-… NM_004694.5:c.-7-1874_-7-1873del	N/A	Intron Variant
SLC16A6 transcript variant X2	XM_011525461.4:c.-7-1874_… XM_011525461.4:c.-7-1874_-7-1873del	N/A	Intron Variant
SLC16A6 transcript variant X4	XM_017025292.3:c.-8+706_-… XM_017025292.3:c.-8+706_-8+707del	N/A	Intron Variant
SLC16A6 transcript variant X1	XM_024451021.2:c.51-1874_… XM_024451021.2:c.51-1874_51-1873del	N/A	Intron Variant
SLC16A6 transcript variant X3	XM_047437020.1:c.-8+800_-… XM_047437020.1:c.-8+800_-8+801del	N/A	Intron Variant

Gene: ARSG, arylsulfatase G (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ARSG transcript variant 7	NM_001352903.2:c.-552+207… NM_001352903.2:c.-552+20775_-552+20776del	N/A	Intron Variant
ARSG transcript variant 8	NM_001352904.2:c.-552+207… NM_001352904.2:c.-552+20775_-552+20776del	N/A	Intron Variant
ARSG transcript variant 1	NM_014960.5:c.-552+20775_… NM_014960.5:c.-552+20775_-552+20776del	N/A	Intron Variant
ARSG transcript variant 2	NM_001267727.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant 3	NM_001352899.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant 4	NM_001352900.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant 5	NM_001352901.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant 6	NM_001352902.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant 9	NM_001352905.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant 10	NM_001352906.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant 11	NM_001352907.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant 12	NM_001352909.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant 13	NM_001352910.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X2	XM_047435632.1:c.-552+207… XM_047435632.1:c.-552+20775_-552+20776del	N/A	Intron Variant
ARSG transcript variant X11	XM_047435639.1:c.-552+207… XM_047435639.1:c.-552+20775_-552+20776del	N/A	Intron Variant
ARSG transcript variant X17	XM_047435644.1:c.-552+207… XM_047435644.1:c.-552+20775_-552+20776del	N/A	Intron Variant
ARSG transcript variant X18	XM_047435645.1:c.-552+207… XM_047435645.1:c.-552+20775_-552+20776del	N/A	Intron Variant
ARSG transcript variant X22	XM_047435647.1:c.-552+207… XM_047435647.1:c.-552+20775_-552+20776del	N/A	Intron Variant
ARSG transcript variant X24	XM_047435649.1:c.-552+207… XM_047435649.1:c.-552+20775_-552+20776del	N/A	Intron Variant
ARSG transcript variant X29	XM_047435653.1:c.-552+207… XM_047435653.1:c.-552+20775_-552+20776del	N/A	Intron Variant
ARSG transcript variant X31	XM_047435655.1:c.-552+207… XM_047435655.1:c.-552+20775_-552+20776del	N/A	Intron Variant
ARSG transcript variant X1	XM_011524536.3:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X4	XM_011524537.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X28	XM_011524546.3:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X3	XM_017024360.3:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X13	XM_017024365.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X20	XM_017024368.2:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X5	XM_047435633.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X6	XM_047435634.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X7	XM_047435635.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X8	XM_047435636.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X9	XM_047435637.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X10	XM_047435638.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X12	XM_047435640.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X14	XM_047435641.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X15	XM_047435642.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X16	XM_047435643.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X19	XM_047435646.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X23	XM_047435648.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X25	XM_047435650.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X26	XM_047435651.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X27	XM_047435652.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X30	XM_047435654.1:c.	N/A	Genic Upstream Transcript Variant
ARSG transcript variant X21	XR_007065287.1:n.	N/A	Genic Upstream Transcript Variant

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.

Not Reported in ClinVar

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	AGA=	delGA
GRCh38.p14 chr 17	NC_000017.11:g.68280200_68280202=	NC_000017.11:g.68280201_68280202del
GRCh37.p13 chr 17	NC_000017.10:g.66276341_66276343=	NC_000017.10:g.66276342_66276343del
ARSG RefSeqGene	NG_032814.2:g.26112_26114=	NG_032814.2:g.26113_26114del
GRCh37.p13 chr 17 fix patch HG747_PATCH	NW_003871088.1:g.340211_340213=	NW_003871088.1:g.340212_340213del
SLC16A6 transcript variant 1	NM_001174166.1:c.-7-1873=	NM_001174166.1:c.-7-1874_-7-1873del
SLC16A6 transcript variant 1	NM_001174166.2:c.-7-1873=	NM_001174166.2:c.-7-1874_-7-1873del
ARSG transcript variant 7	NM_001352903.2:c.-552+20774=	NM_001352903.2:c.-552+20775_-552+20776del
ARSG transcript variant 8	NM_001352904.2:c.-552+20774=	NM_001352904.2:c.-552+20775_-552+20776del
SLC16A6 transcript variant 2	NM_004694.4:c.-7-1873=	NM_004694.4:c.-7-1874_-7-1873del
SLC16A6 transcript variant 2	NM_004694.5:c.-7-1873=	NM_004694.5:c.-7-1874_-7-1873del
ARSG transcript variant 1	NM_014960.4:c.-552+20774=	NM_014960.4:c.-552+20775_-552+20776del
ARSG transcript variant 1	NM_014960.5:c.-552+20774=	NM_014960.5:c.-552+20775_-552+20776del
ARSG transcript variant X1	XM_005257170.1:c.-552+20774=	XM_005257170.1:c.-552+20775_-552+20776del
ARSG transcript variant X3	XM_005257172.1:c.-552+20774=	XM_005257172.1:c.-552+20775_-552+20776del
SLC16A6 transcript variant X2	XM_011525461.4:c.-7-1873=	XM_011525461.4:c.-7-1874_-7-1873del
SLC16A6 transcript variant X4	XM_017025292.3:c.-8+707=	XM_017025292.3:c.-8+706_-8+707del
SLC16A6 transcript variant X1	XM_024451021.2:c.51-1873=	XM_024451021.2:c.51-1874_51-1873del
ARSG transcript variant X2	XM_047435632.1:c.-552+20774=	XM_047435632.1:c.-552+20775_-552+20776del
ARSG transcript variant X11	XM_047435639.1:c.-552+20774=	XM_047435639.1:c.-552+20775_-552+20776del
ARSG transcript variant X17	XM_047435644.1:c.-552+20774=	XM_047435644.1:c.-552+20775_-552+20776del
ARSG transcript variant X18	XM_047435645.1:c.-552+20774=	XM_047435645.1:c.-552+20775_-552+20776del
ARSG transcript variant X22	XM_047435647.1:c.-552+20774=	XM_047435647.1:c.-552+20775_-552+20776del
ARSG transcript variant X24	XM_047435649.1:c.-552+20774=	XM_047435649.1:c.-552+20775_-552+20776del
ARSG transcript variant X29	XM_047435653.1:c.-552+20774=	XM_047435653.1:c.-552+20775_-552+20776del
ARSG transcript variant X31	XM_047435655.1:c.-552+20774=	XM_047435655.1:c.-552+20775_-552+20776del
SLC16A6 transcript variant X3	XM_047437020.1:c.-8+801=	XM_047437020.1:c.-8+800_-8+801del

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#.

2 SubSNP, 2 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss2951894260	Oct 12, 2018 (152)
2	GNOMAD	ss4314788204	Apr 27, 2021 (155)
3	gnomAD - Genomes	NC_000017.11 - 68280200	Apr 27, 2021 (155)
4	ALFA	NC_000017.11 - 68280200	Apr 27, 2021 (155)

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
ss2951894260	NC_000017.10:66276340:AG:	NC_000017.11:68280199:AGA:A	(self)
512415445, ss4314788204	NC_000017.11:68280199:AG:	NC_000017.11:68280199:AGA:A	(self)
9111143110	NC_000017.11:68280199:AGA:A	NC_000017.11:68280199:AGA:A	(self)

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

No publications for rs1489735173

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1489735173