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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.

rs60129285

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:120432929-120432944 (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
delAAA / delAA / delA / dupA / dup…

delAAA / delAA / delA / dupA / dupAA

Variation Type
Indel Insertion and Deletion
Frequency
delA=0.12170 (1303/10707, ALFA)
delA=0.45 (18/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LAMP2 : 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 Alt HMOZ HTRZ HWEP
Total Global 10707 AAAAAAAAAAAAAAAA=0.87765 AAAAAAAAAAAAAA=0.00019, AAAAAAAAAAAAAAA=0.12170, AAAAAAAAAAAAAAAAA=0.00047, AAAAAAAAAAAAAAAAAA=0.00000 0.825239 0.069379 0.105382 32
European Sub 7941 AAAAAAAAAAAAAAAA=0.8357 AAAAAAAAAAAAAA=0.0003, AAAAAAAAAAAAAAA=0.1635, AAAAAAAAAAAAAAAAA=0.0006, AAAAAAAAAAAAAAAAAA=0.0000 0.76481 0.093165 0.142025 32
African Sub 1990 AAAAAAAAAAAAAAAA=1.0000 AAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAAA=0.0000 1.0 0.0 0.0 N/A
African Others Sub 86 AAAAAAAAAAAAAAAA=1.00 AAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
African American Sub 1904 AAAAAAAAAAAAAAAA=1.0000 AAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAA=0.0000, AAAAAAAAAAAAAAAAAA=0.0000 1.0 0.0 0.0 N/A
Asian Sub 60 AAAAAAAAAAAAAAAA=1.00 AAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
East Asian Sub 44 AAAAAAAAAAAAAAAA=1.00 AAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 16 AAAAAAAAAAAAAAAA=1.00 AAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 82 AAAAAAAAAAAAAAAA=1.00 AAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
Latin American 2 Sub 330 AAAAAAAAAAAAAAAA=1.000 AAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAA=0.000 1.0 0.0 0.0 N/A
South Asian Sub 46 AAAAAAAAAAAAAAAA=1.00 AAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAA=0.00, AAAAAAAAAAAAAAAAAA=0.00 1.0 0.0 0.0 N/A
Other Sub 258 AAAAAAAAAAAAAAAA=0.981 AAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAA=0.019, AAAAAAAAAAAAAAAAA=0.000, AAAAAAAAAAAAAAAAAA=0.000 0.976744 0.015504 0.007752 32


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
Allele Frequency Aggregator Total Global 10707 (A)16=0.87765 delAA=0.00019, delA=0.12170, dupA=0.00047, dupAA=0.00000
Allele Frequency Aggregator European Sub 7941 (A)16=0.8357 delAA=0.0003, delA=0.1635, dupA=0.0006, dupAA=0.0000
Allele Frequency Aggregator African Sub 1990 (A)16=1.0000 delAA=0.0000, delA=0.0000, dupA=0.0000, dupAA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 330 (A)16=1.000 delAA=0.000, delA=0.000, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator Other Sub 258 (A)16=0.981 delAA=0.000, delA=0.019, dupA=0.000, dupAA=0.000
Allele Frequency Aggregator Latin American 1 Sub 82 (A)16=1.00 delAA=0.00, delA=0.00, dupA=0.00, dupAA=0.00
Allele Frequency Aggregator Asian Sub 60 (A)16=1.00 delAA=0.00, delA=0.00, dupA=0.00, dupAA=0.00
Allele Frequency Aggregator South Asian Sub 46 (A)16=1.00 delAA=0.00, delA=0.00, dupA=0.00, dupAA=0.00
The Danish reference pan genome Danish Study-wide 40 (A)16=0.55 delA=0.45
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.p14 chr X NC_000023.11:g.120432942_120432944del
GRCh38.p14 chr X NC_000023.11:g.120432943_120432944del
GRCh38.p14 chr X NC_000023.11:g.120432944del
GRCh38.p14 chr X NC_000023.11:g.120432944dup
GRCh38.p14 chr X NC_000023.11:g.120432943_120432944dup
GRCh37.p13 chr X NC_000023.10:g.119566797_119566799del
GRCh37.p13 chr X NC_000023.10:g.119566798_119566799del
GRCh37.p13 chr X NC_000023.10:g.119566799del
GRCh37.p13 chr X NC_000023.10:g.119566799dup
GRCh37.p13 chr X NC_000023.10:g.119566798_119566799dup
LAMP2 RefSeqGene (LRG_749) NG_007995.1:g.41419_41421del
LAMP2 RefSeqGene (LRG_749) NG_007995.1:g.41420_41421del
LAMP2 RefSeqGene (LRG_749) NG_007995.1:g.41421del
LAMP2 RefSeqGene (LRG_749) NG_007995.1:g.41421dup
LAMP2 RefSeqGene (LRG_749) NG_007995.1:g.41420_41421dup
Gene: LAMP2, lysosomal associated membrane protein 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LAMP2 transcript variant C NM_001122606.1:c.1094-430…

NM_001122606.1:c.1094-4305_1094-4303del

N/A Intron Variant
LAMP2 transcript variant A NM_002294.3:c.1094-1469_1…

NM_002294.3:c.1094-1469_1094-1467del

N/A Intron Variant
LAMP2 transcript variant B NM_013995.2:c. N/A Genic Downstream Transcript 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.

Not Reported in ClinVar
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 (A)16= delAAA delAA delA dupA dupAA
GRCh38.p14 chr X NC_000023.11:g.120432929_120432944= NC_000023.11:g.120432942_120432944del NC_000023.11:g.120432943_120432944del NC_000023.11:g.120432944del NC_000023.11:g.120432944dup NC_000023.11:g.120432943_120432944dup
GRCh37.p13 chr X NC_000023.10:g.119566784_119566799= NC_000023.10:g.119566797_119566799del NC_000023.10:g.119566798_119566799del NC_000023.10:g.119566799del NC_000023.10:g.119566799dup NC_000023.10:g.119566798_119566799dup
LAMP2 RefSeqGene (LRG_749) NG_007995.1:g.41406_41421= NG_007995.1:g.41419_41421del NG_007995.1:g.41420_41421del NG_007995.1:g.41421del NG_007995.1:g.41421dup NG_007995.1:g.41420_41421dup
LAMP2 transcript variant C NM_001122606.1:c.1094-4303= NM_001122606.1:c.1094-4305_1094-4303del NM_001122606.1:c.1094-4304_1094-4303del NM_001122606.1:c.1094-4303del NM_001122606.1:c.1094-4303dup NM_001122606.1:c.1094-4304_1094-4303dup
LAMP2 transcript variant A NM_002294.2:c.1094-1467= NM_002294.2:c.1094-1469_1094-1467del NM_002294.2:c.1094-1468_1094-1467del NM_002294.2:c.1094-1467del NM_002294.2:c.1094-1467dup NM_002294.2:c.1094-1468_1094-1467dup
LAMP2 transcript variant A NM_002294.3:c.1094-1467= NM_002294.3:c.1094-1469_1094-1467del NM_002294.3:c.1094-1468_1094-1467del NM_002294.3:c.1094-1467del NM_002294.3:c.1094-1467dup NM_002294.3:c.1094-1468_1094-1467dup
LAMP2 transcript variant X1 XM_005262412.1:c.761-4303= XM_005262412.1:c.761-4305_761-4303del XM_005262412.1:c.761-4304_761-4303del XM_005262412.1:c.761-4303del XM_005262412.1:c.761-4303dup XM_005262412.1:c.761-4304_761-4303dup
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#.

26 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 ABI ss43804687 Oct 12, 2018 (152)
2 HGSV ss81141310 Sep 08, 2015 (146)
3 HGSV ss81965615 Sep 08, 2015 (146)
4 PJP ss295462659 May 09, 2011 (134)
5 GMI ss478856464 May 04, 2012 (137)
6 SSMP ss664541084 Apr 01, 2015 (144)
7 EVA_GENOME_DK ss1577631498 Apr 01, 2015 (144)
8 SWEGEN ss3020545070 Nov 08, 2017 (151)
9 MCHAISSO ss3064379191 Nov 08, 2017 (151)
10 URBANLAB ss3651327257 Oct 12, 2018 (152)
11 EVA ss3836296089 Apr 27, 2020 (154)
12 GNOMAD ss4377898841 Apr 27, 2021 (155)
13 GNOMAD ss4377898842 Apr 27, 2021 (155)
14 GNOMAD ss4377898843 Apr 27, 2021 (155)
15 GNOMAD ss4377898844 Apr 27, 2021 (155)
16 TOMMO_GENOMICS ss5236064555 Apr 27, 2021 (155)
17 TOMMO_GENOMICS ss5236064556 Apr 27, 2021 (155)
18 1000G_HIGH_COVERAGE ss5313761121 Oct 16, 2022 (156)
19 1000G_HIGH_COVERAGE ss5313761122 Oct 16, 2022 (156)
20 1000G_HIGH_COVERAGE ss5313761123 Oct 16, 2022 (156)
21 HUGCELL_USP ss5505190149 Oct 16, 2022 (156)
22 HUGCELL_USP ss5505190151 Oct 16, 2022 (156)
23 HUGCELL_USP ss5505190152 Oct 16, 2022 (156)
24 TOMMO_GENOMICS ss5798379649 Oct 16, 2022 (156)
25 TOMMO_GENOMICS ss5798379650 Oct 16, 2022 (156)
26 EVA ss5857184111 Oct 16, 2022 (156)
27 The Danish reference pan genome NC_000023.10 - 119566784 Apr 27, 2020 (154)
28 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 590112448 (NC_000023.11:120432928::A 3344/68298)
Row 590112449 (NC_000023.11:120432928::AA 6/68361)
Row 590112450 (NC_000023.11:120432928:A: 23922/68091)...

- Apr 27, 2021 (155)
29 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 590112448 (NC_000023.11:120432928::A 3344/68298)
Row 590112449 (NC_000023.11:120432928::AA 6/68361)
Row 590112450 (NC_000023.11:120432928:A: 23922/68091)...

- Apr 27, 2021 (155)
30 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 590112448 (NC_000023.11:120432928::A 3344/68298)
Row 590112449 (NC_000023.11:120432928::AA 6/68361)
Row 590112450 (NC_000023.11:120432928:A: 23922/68091)...

- Apr 27, 2021 (155)
31 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 590112448 (NC_000023.11:120432928::A 3344/68298)
Row 590112449 (NC_000023.11:120432928::AA 6/68361)
Row 590112450 (NC_000023.11:120432928:A: 23922/68091)...

- Apr 27, 2021 (155)
32 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 590112448 (NC_000023.11:120432928::A 3344/68298)
Row 590112449 (NC_000023.11:120432928::AA 6/68361)
Row 590112450 (NC_000023.11:120432928:A: 23922/68091)...

- Apr 27, 2021 (155)
33 8.3KJPN

Submission ignored due to conflicting rows:
Row 94033862 (NC_000023.10:119566783:A: 5162/12830)
Row 94033863 (NC_000023.10:119566783::A 21/12830)

- Apr 27, 2021 (155)
34 8.3KJPN

Submission ignored due to conflicting rows:
Row 94033862 (NC_000023.10:119566783:A: 5162/12830)
Row 94033863 (NC_000023.10:119566783::A 21/12830)

- Apr 27, 2021 (155)
35 14KJPN

Submission ignored due to conflicting rows:
Row 132216753 (NC_000023.11:120432928:A: 8932/22207)
Row 132216754 (NC_000023.11:120432928::A 28/22207)

- Oct 16, 2022 (156)
36 14KJPN

Submission ignored due to conflicting rows:
Row 132216753 (NC_000023.11:120432928:A: 8932/22207)
Row 132216754 (NC_000023.11:120432928::A 28/22207)

- Oct 16, 2022 (156)
37 ALFA NC_000023.11 - 120432929 Apr 27, 2021 (155)
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).

Associated ID History Updated (Build)
rs201786743 May 11, 2012 (137)
rs376171397 May 13, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss4377898844 NC_000023.11:120432928:AAA: NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAA

(self)
ss4377898843, ss5313761123, ss5505190151 NC_000023.11:120432928:AA: NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAA

(self)
9505465349 NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAA

NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAA

(self)
ss81141310, ss81965615 NC_000023.8:119348680:A: NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA

(self)
ss478856464 NC_000023.9:119450811:A: NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA

(self)
ss295462659 NC_000023.9:119450826:A: NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA

(self)
1344494, ss664541084, ss1577631498, ss3020545070, ss5236064555 NC_000023.10:119566783:A: NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA

(self)
ss3064379191, ss5313761121, ss5505190149, ss5798379649, ss5857184111 NC_000023.11:120432928:A: NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA

(self)
9505465349 NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA

NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA

(self)
ss3836296089, ss5236064556 NC_000023.10:119566783::A NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA

(self)
ss3651327257, ss4377898841, ss5313761122, ss5505190152, ss5798379650 NC_000023.11:120432928::A NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA

(self)
9505465349 NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA

NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA

(self)
ss43804687 NT_011786.16:3834509::A NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA

(self)
ss4377898842 NC_000023.11:120432928::AA NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA

(self)
9505465349 NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA

NC_000023.11:120432928:AAAAAAAAAAA…

NC_000023.11:120432928:AAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA

(self)
Help

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

No publications for rs60129285

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.post820+afb47a3d