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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.

rs372555243

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:88844337-88844345 (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
delAA / delA / dupA
Variation Type
Indel Insertion and Deletion
Frequency
dupA=0.001385 (319/230396, GnomAD_exome)
dupA=0.00004 (1/28258, 14KJPN)
dupA=0.00061 (14/22926, ALFA) (+ 2 more)
dupA=0.00006 (1/16760, 8.3KJPN)
dupA=0.0036 (18/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNGTT : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 22926 AAAAAAAAA=0.99891 AAAAAAA=0.00000, AAAAAAAA=0.00048, AAAAAAAAAA=0.00061
European Sub 15746 AAAAAAAAA=0.99917 AAAAAAA=0.00000, AAAAAAAA=0.00025, AAAAAAAAAA=0.00057
African Sub 3390 AAAAAAAAA=0.9982 AAAAAAA=0.0000, AAAAAAAA=0.0012, AAAAAAAAAA=0.0006
African Others Sub 116 AAAAAAAAA=0.991 AAAAAAA=0.000, AAAAAAAA=0.009, AAAAAAAAAA=0.000
African American Sub 3274 AAAAAAAAA=0.9985 AAAAAAA=0.0000, AAAAAAAA=0.0009, AAAAAAAAAA=0.0006
Asian Sub 168 AAAAAAAAA=1.000 AAAAAAA=0.000, AAAAAAAA=0.000, AAAAAAAAAA=0.000
East Asian Sub 112 AAAAAAAAA=1.000 AAAAAAA=0.000, AAAAAAAA=0.000, AAAAAAAAAA=0.000
Other Asian Sub 56 AAAAAAAAA=1.00 AAAAAAA=0.00, AAAAAAAA=0.00, AAAAAAAAAA=0.00
Latin American 1 Sub 144 AAAAAAAAA=1.000 AAAAAAA=0.000, AAAAAAAA=0.000, AAAAAAAAAA=0.000
Latin American 2 Sub 610 AAAAAAAAA=1.000 AAAAAAA=0.000, AAAAAAAA=0.000, AAAAAAAAAA=0.000
South Asian Sub 98 AAAAAAAAA=1.00 AAAAAAA=0.00, AAAAAAAA=0.00, AAAAAAAAAA=0.00
Other Sub 2770 AAAAAAAAA=0.9978 AAAAAAA=0.0000, AAAAAAAA=0.0011, AAAAAAAAAA=0.0011


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
gnomAD - Exomes Global Study-wide 230396 -

No frequency provided

dupA=0.001385
gnomAD - Exomes European Sub 125768 -

No frequency provided

dupA=0.000127
gnomAD - Exomes Asian Sub 43940 -

No frequency provided

dupA=0.00009
gnomAD - Exomes American Sub 30656 -

No frequency provided

dupA=0.00069
gnomAD - Exomes African Sub 15674 -

No frequency provided

dupA=0.01754
gnomAD - Exomes Ashkenazi Jewish Sub 8860 -

No frequency provided

dupA=0.0000
gnomAD - Exomes Other Sub 5498 -

No frequency provided

dupA=0.0005
14KJPN JAPANESE Study-wide 28258 -

No frequency provided

dupA=0.00004
Allele Frequency Aggregator Total Global 22926 (A)9=0.99891 delAA=0.00000, delA=0.00048, dupA=0.00061
Allele Frequency Aggregator European Sub 15746 (A)9=0.99917 delAA=0.00000, delA=0.00025, dupA=0.00057
Allele Frequency Aggregator African Sub 3390 (A)9=0.9982 delAA=0.0000, delA=0.0012, dupA=0.0006
Allele Frequency Aggregator Other Sub 2770 (A)9=0.9978 delAA=0.0000, delA=0.0011, dupA=0.0011
Allele Frequency Aggregator Latin American 2 Sub 610 (A)9=1.000 delAA=0.000, delA=0.000, dupA=0.000
Allele Frequency Aggregator Asian Sub 168 (A)9=1.000 delAA=0.000, delA=0.000, dupA=0.000
Allele Frequency Aggregator Latin American 1 Sub 144 (A)9=1.000 delAA=0.000, delA=0.000, dupA=0.000
Allele Frequency Aggregator South Asian Sub 98 (A)9=1.00 delAA=0.00, delA=0.00, dupA=0.00
8.3KJPN JAPANESE Study-wide 16760 -

No frequency provided

dupA=0.00006
1000Genomes Global Study-wide 5008 -

No frequency provided

dupA=0.0036
1000Genomes African Sub 1322 -

No frequency provided

dupA=0.0121
1000Genomes East Asian Sub 1008 -

No frequency provided

dupA=0.0000
1000Genomes Europe Sub 1006 -

No frequency provided

dupA=0.0000
1000Genomes South Asian Sub 978 -

No frequency provided

dupA=0.000
1000Genomes American Sub 694 -

No frequency provided

dupA=0.003
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 6 NC_000006.12:g.88844344_88844345del
GRCh38.p14 chr 6 NC_000006.12:g.88844345del
GRCh38.p14 chr 6 NC_000006.12:g.88844345dup
GRCh37.p13 chr 6 NC_000006.11:g.89554063_89554064del
GRCh37.p13 chr 6 NC_000006.11:g.89554064del
GRCh37.p13 chr 6 NC_000006.11:g.89554064dup
Gene: RNGTT, RNA guanylyltransferase and 5'-phosphatase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RNGTT transcript variant 2 NM_001286426.2:c.1269+19_…

NM_001286426.2:c.1269+19_1269+20del

N/A Intron Variant
RNGTT transcript variant 3 NM_001286428.2:c.1089+19_…

NM_001286428.2:c.1089+19_1089+20del

N/A Intron Variant
RNGTT transcript variant 1 NM_003800.5:c.1269+19_126…

NM_003800.5:c.1269+19_1269+20del

N/A Intron Variant
RNGTT transcript variant X1 XM_047419442.1:c.1269+19_…

XM_047419442.1:c.1269+19_1269+20del

N/A Intron Variant
RNGTT transcript variant X2 XM_047419443.1:c.1269+19_…

XM_047419443.1:c.1269+19_1269+20del

N/A Intron 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)9= delAA delA dupA
GRCh38.p14 chr 6 NC_000006.12:g.88844337_88844345= NC_000006.12:g.88844344_88844345del NC_000006.12:g.88844345del NC_000006.12:g.88844345dup
GRCh37.p13 chr 6 NC_000006.11:g.89554056_89554064= NC_000006.11:g.89554063_89554064del NC_000006.11:g.89554064del NC_000006.11:g.89554064dup
RNGTT transcript variant 2 NM_001286426.2:c.1269+20= NM_001286426.2:c.1269+19_1269+20del NM_001286426.2:c.1269+20del NM_001286426.2:c.1269+20dup
RNGTT transcript variant 3 NM_001286428.2:c.1089+20= NM_001286428.2:c.1089+19_1089+20del NM_001286428.2:c.1089+20del NM_001286428.2:c.1089+20dup
RNGTT transcript NM_003800.3:c.1269+20= NM_003800.3:c.1269+19_1269+20del NM_003800.3:c.1269+20del NM_003800.3:c.1269+20dup
RNGTT transcript variant 1 NM_003800.5:c.1269+20= NM_003800.5:c.1269+19_1269+20del NM_003800.5:c.1269+20del NM_003800.5:c.1269+20dup
RNGTT transcript variant X1 XM_005248767.1:c.1269+20= XM_005248767.1:c.1269+19_1269+20del XM_005248767.1:c.1269+20del XM_005248767.1:c.1269+20dup
RNGTT transcript variant X1 XM_047419442.1:c.1269+20= XM_047419442.1:c.1269+19_1269+20del XM_047419442.1:c.1269+20del XM_047419442.1:c.1269+20dup
RNGTT transcript variant X2 XM_047419443.1:c.1269+20= XM_047419443.1:c.1269+19_1269+20del XM_047419443.1:c.1269+20del XM_047419443.1:c.1269+20dup
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#.

16 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 WARNICH_LAB ss678332673 Apr 25, 2013 (138)
2 1000GENOMES ss1375816825 Aug 21, 2014 (142)
3 EVA_EXAC ss1711831710 Apr 01, 2015 (144)
4 EVA_EXAC ss1711831711 Apr 01, 2015 (144)
5 EVA ss3986353176 Apr 26, 2021 (155)
6 GNOMAD ss4146447659 Apr 26, 2021 (155)
7 GNOMAD ss4146447660 Apr 26, 2021 (155)
8 TOPMED ss4712185635 Apr 26, 2021 (155)
9 TOPMED ss4712185636 Apr 26, 2021 (155)
10 TOPMED ss4712185637 Apr 26, 2021 (155)
11 TOMMO_GENOMICS ss5178694625 Apr 26, 2021 (155)
12 1000G_HIGH_COVERAGE ss5269385307 Oct 14, 2022 (156)
13 HUGCELL_USP ss5466920257 Oct 14, 2022 (156)
14 HUGCELL_USP ss5466920258 Oct 14, 2022 (156)
15 SANFORD_IMAGENETICS ss5640943397 Oct 14, 2022 (156)
16 TOMMO_GENOMICS ss5717216914 Oct 14, 2022 (156)
17 1000Genomes NC_000006.11 - 89554056 Oct 12, 2018 (152)
18 ExAC

Submission ignored due to conflicting rows:
Row 8462188 (NC_000006.11:89554055::A 194/114886)
Row 8462189 (NC_000006.11:89554055:A: 39/114886)

- Oct 12, 2018 (152)
19 ExAC

Submission ignored due to conflicting rows:
Row 8462188 (NC_000006.11:89554055::A 194/114886)
Row 8462189 (NC_000006.11:89554055:A: 39/114886)

- Oct 12, 2018 (152)
20 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 232975743 (NC_000006.12:88844336::A 690/139564)
Row 232975744 (NC_000006.12:88844336:A: 28/139562)
Row 232975745 (NC_000006.12:88844336:AA: 1/139568)

- Apr 26, 2021 (155)
21 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 232975743 (NC_000006.12:88844336::A 690/139564)
Row 232975744 (NC_000006.12:88844336:A: 28/139562)
Row 232975745 (NC_000006.12:88844336:AA: 1/139568)

- Apr 26, 2021 (155)
22 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 232975743 (NC_000006.12:88844336::A 690/139564)
Row 232975744 (NC_000006.12:88844336:A: 28/139562)
Row 232975745 (NC_000006.12:88844336:AA: 1/139568)

- Apr 26, 2021 (155)
23 gnomAD - Exomes NC_000006.11 - 89554056 Jul 13, 2019 (153)
24 8.3KJPN NC_000006.11 - 89554056 Apr 26, 2021 (155)
25 14KJPN NC_000006.12 - 88844337 Oct 14, 2022 (156)
26 TopMed

Submission ignored due to conflicting rows:
Row 549563193 (NC_000006.12:88844336::A 1423/264690)
Row 549563194 (NC_000006.12:88844336:A: 45/264690)
Row 549563195 (NC_000006.12:88844336:AA: 1/264690)

- Apr 26, 2021 (155)
27 TopMed

Submission ignored due to conflicting rows:
Row 549563193 (NC_000006.12:88844336::A 1423/264690)
Row 549563194 (NC_000006.12:88844336:A: 45/264690)
Row 549563195 (NC_000006.12:88844336:AA: 1/264690)

- Apr 26, 2021 (155)
28 TopMed

Submission ignored due to conflicting rows:
Row 549563193 (NC_000006.12:88844336::A 1423/264690)
Row 549563194 (NC_000006.12:88844336:A: 45/264690)
Row 549563195 (NC_000006.12:88844336:AA: 1/264690)

- Apr 26, 2021 (155)
29 ALFA NC_000006.12 - 88844337 Apr 26, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss4146447660, ss4712185637 NC_000006.12:88844336:AA: NC_000006.12:88844336:AAAAAAAAA:AA…

NC_000006.12:88844336:AAAAAAAAA:AAAAAAA

(self)
12748033669 NC_000006.12:88844336:AAAAAAAAA:AA…

NC_000006.12:88844336:AAAAAAAAA:AAAAAAA

NC_000006.12:88844336:AAAAAAAAA:AA…

NC_000006.12:88844336:AAAAAAAAA:AAAAAAA

(self)
ss1711831711 NC_000006.11:89554055:A: NC_000006.12:88844336:AAAAAAAAA:AA…

NC_000006.12:88844336:AAAAAAAAA:AAAAAAAA

(self)
ss4712185636, ss5269385307, ss5466920258 NC_000006.12:88844336:A: NC_000006.12:88844336:AAAAAAAAA:AA…

NC_000006.12:88844336:AAAAAAAAA:AAAAAAAA

(self)
12748033669 NC_000006.12:88844336:AAAAAAAAA:AA…

NC_000006.12:88844336:AAAAAAAAA:AAAAAAAA

NC_000006.12:88844336:AAAAAAAAA:AA…

NC_000006.12:88844336:AAAAAAAAA:AAAAAAAA

(self)
33014507, 5093828, 36663932, ss678332673, ss1375816825, ss1711831710, ss3986353176, ss5178694625, ss5640943397 NC_000006.11:89554055::A NC_000006.12:88844336:AAAAAAAAA:AA…

NC_000006.12:88844336:AAAAAAAAA:AAAAAAAAAA

(self)
51054018, ss4146447659, ss4712185635, ss5466920257, ss5717216914 NC_000006.12:88844336::A NC_000006.12:88844336:AAAAAAAAA:AA…

NC_000006.12:88844336:AAAAAAAAA:AAAAAAAAAA

(self)
12748033669 NC_000006.12:88844336:AAAAAAAAA:AA…

NC_000006.12:88844336:AAAAAAAAA:AAAAAAAAAA

NC_000006.12:88844336:AAAAAAAAA:AA…

NC_000006.12:88844336:AAAAAAAAA:AAAAAAAAAA

(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 rs372555243

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.post761+d5e8e07