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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.

rs1369955901

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:9104681-9104690 (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
delTCTC / delTC / dupTC
Variation Type
Indel Insertion and Deletion
Frequency
delTCTC=0.00025 (7/28258, 14KJPN)
delTCTC=0.00024 (4/16760, 8.3KJPN)
delTCTC=0.00000 (0/14046, ALFA) (+ 3 more)
delTC=0.00000 (0/14046, ALFA)
dupTC=0.00000 (0/14046, ALFA)
delTCTC=0.0033 (6/1832, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NDUFV2 : 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 14046 TCTCTCTCTC=1.00000 TCTCTC=0.00000, TCTCTCTC=0.00000, TCTCTCTCTCTC=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 TCTCTCTCTC=1.0000 TCTCTC=0.0000, TCTCTCTC=0.0000, TCTCTCTCTCTC=0.0000 1.0 0.0 0.0 N/A
African Sub 2894 TCTCTCTCTC=1.0000 TCTCTC=0.0000, TCTCTCTC=0.0000, TCTCTCTCTCTC=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 TCTCTCTCTC=1.000 TCTCTC=0.000, TCTCTCTC=0.000, TCTCTCTCTCTC=0.000 1.0 0.0 0.0 N/A
African American Sub 2780 TCTCTCTCTC=1.0000 TCTCTC=0.0000, TCTCTCTC=0.0000, TCTCTCTCTCTC=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 TCTCTCTCTC=1.000 TCTCTC=0.000, TCTCTCTC=0.000, TCTCTCTCTCTC=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 TCTCTCTCTC=1.00 TCTCTC=0.00, TCTCTCTC=0.00, TCTCTCTCTCTC=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 TCTCTCTCTC=1.00 TCTCTC=0.00, TCTCTCTC=0.00, TCTCTCTCTCTC=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TCTCTCTCTC=1.000 TCTCTC=0.000, TCTCTCTC=0.000, TCTCTCTCTCTC=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TCTCTCTCTC=1.000 TCTCTC=0.000, TCTCTCTC=0.000, TCTCTCTCTCTC=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 TCTCTCTCTC=1.00 TCTCTC=0.00, TCTCTCTC=0.00, TCTCTCTCTCTC=0.00 1.0 0.0 0.0 N/A
Other Sub 496 TCTCTCTCTC=1.000 TCTCTC=0.000, TCTCTCTC=0.000, TCTCTCTCTCTC=0.000 1.0 0.0 0.0 N/A


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
14KJPN JAPANESE Study-wide 28258 (TC)5=0.99975 delTCTC=0.00025
8.3KJPN JAPANESE Study-wide 16760 (TC)5=0.99976 delTCTC=0.00024
Allele Frequency Aggregator Total Global 14046 (TC)5=1.00000 delTCTC=0.00000, delTC=0.00000, dupTC=0.00000
Allele Frequency Aggregator European Sub 9690 (TC)5=1.0000 delTCTC=0.0000, delTC=0.0000, dupTC=0.0000
Allele Frequency Aggregator African Sub 2894 (TC)5=1.0000 delTCTC=0.0000, delTC=0.0000, dupTC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (TC)5=1.000 delTCTC=0.000, delTC=0.000, dupTC=0.000
Allele Frequency Aggregator Other Sub 496 (TC)5=1.000 delTCTC=0.000, delTC=0.000, dupTC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (TC)5=1.000 delTCTC=0.000, delTC=0.000, dupTC=0.000
Allele Frequency Aggregator Asian Sub 112 (TC)5=1.000 delTCTC=0.000, delTC=0.000, dupTC=0.000
Allele Frequency Aggregator South Asian Sub 98 (TC)5=1.00 delTCTC=0.00, delTC=0.00, dupTC=0.00
Korean Genome Project KOREAN Study-wide 1832 (TC)5=0.9967 delTCTC=0.0033
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 18 NC_000018.10:g.9104681TC[3]
GRCh38.p14 chr 18 NC_000018.10:g.9104681TC[4]
GRCh38.p14 chr 18 NC_000018.10:g.9104681TC[6]
GRCh37.p13 chr 18 NC_000018.9:g.9104679TC[3]
GRCh37.p13 chr 18 NC_000018.9:g.9104679TC[4]
GRCh37.p13 chr 18 NC_000018.9:g.9104679TC[6]
NDUFV2 RefSeqGene NG_013355.1:g.7052TC[3]
NDUFV2 RefSeqGene NG_013355.1:g.7052TC[4]
NDUFV2 RefSeqGene NG_013355.1:g.7052TC[6]
Gene: NDUFV2, NADH:ubiquinone oxidoreductase core subunit V2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NDUFV2 transcript NM_021074.5:c.54+1884TC[3] N/A Intron Variant
NDUFV2 transcript variant X1 XM_017025782.2:c. N/A Genic Upstream Transcript Variant
NDUFV2 transcript variant X2 XR_243808.4:n. 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 (TC)5= delTCTC delTC dupTC
GRCh38.p14 chr 18 NC_000018.10:g.9104681_9104690= NC_000018.10:g.9104681TC[3] NC_000018.10:g.9104681TC[4] NC_000018.10:g.9104681TC[6]
GRCh37.p13 chr 18 NC_000018.9:g.9104679_9104688= NC_000018.9:g.9104679TC[3] NC_000018.9:g.9104679TC[4] NC_000018.9:g.9104679TC[6]
NDUFV2 RefSeqGene NG_013355.1:g.7052_7061= NG_013355.1:g.7052TC[3] NG_013355.1:g.7052TC[4] NG_013355.1:g.7052TC[6]
NDUFV2 transcript NM_021074.4:c.54+1884= NM_021074.4:c.54+1884TC[3] NM_021074.4:c.54+1884TC[4] NM_021074.4:c.54+1884TC[6]
NDUFV2 transcript NM_021074.5:c.54+1884= NM_021074.5:c.54+1884TC[3] NM_021074.5:c.54+1884TC[4] NM_021074.5:c.54+1884TC[6]
NDUFV2 transcript variant X1 XM_005258106.1:c.54+1884= XM_005258106.1:c.54+1884TC[3] XM_005258106.1:c.54+1884TC[4] XM_005258106.1:c.54+1884TC[6]
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#.

11 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 KOGIC ss3979583980 Apr 27, 2020 (154)
2 GNOMAD ss4317943681 Apr 27, 2021 (155)
3 GNOMAD ss4317943682 Apr 27, 2021 (155)
4 GNOMAD ss4317943683 Apr 27, 2021 (155)
5 TOPMED ss5048328177 Apr 27, 2021 (155)
6 TOPMED ss5048328178 Apr 27, 2021 (155)
7 TOPMED ss5048328179 Apr 27, 2021 (155)
8 TOMMO_GENOMICS ss5224114313 Apr 27, 2021 (155)
9 TOMMO_GENOMICS ss5780868131 Oct 16, 2022 (156)
10 YY_MCH ss5816856913 Oct 16, 2022 (156)
11 EVA ss5873153576 Oct 16, 2022 (156)
12 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 517688504 (NC_000018.10:9104680::TC 1/140010)
Row 517688505 (NC_000018.10:9104680:TC: 4/140010)
Row 517688506 (NC_000018.10:9104680:TCTC: 13/140010)

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

Submission ignored due to conflicting rows:
Row 517688504 (NC_000018.10:9104680::TC 1/140010)
Row 517688505 (NC_000018.10:9104680:TC: 4/140010)
Row 517688506 (NC_000018.10:9104680:TCTC: 13/140010)

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

Submission ignored due to conflicting rows:
Row 517688504 (NC_000018.10:9104680::TC 1/140010)
Row 517688505 (NC_000018.10:9104680:TC: 4/140010)
Row 517688506 (NC_000018.10:9104680:TCTC: 13/140010)

- Apr 27, 2021 (155)
15 Korean Genome Project NC_000018.10 - 9104681 Apr 27, 2020 (154)
16 8.3KJPN NC_000018.9 - 9104679 Apr 27, 2021 (155)
17 14KJPN NC_000018.10 - 9104681 Oct 16, 2022 (156)
18 TopMed

Submission ignored due to conflicting rows:
Row 263873840 (NC_000018.10:9104680::TC 2/264690)
Row 263873841 (NC_000018.10:9104680:TC: 3/264690)
Row 263873842 (NC_000018.10:9104680:TCTC: 26/264690)

- Apr 27, 2021 (155)
19 TopMed

Submission ignored due to conflicting rows:
Row 263873840 (NC_000018.10:9104680::TC 2/264690)
Row 263873841 (NC_000018.10:9104680:TC: 3/264690)
Row 263873842 (NC_000018.10:9104680:TCTC: 26/264690)

- Apr 27, 2021 (155)
20 TopMed

Submission ignored due to conflicting rows:
Row 263873840 (NC_000018.10:9104680::TC 2/264690)
Row 263873841 (NC_000018.10:9104680:TC: 3/264690)
Row 263873842 (NC_000018.10:9104680:TCTC: 26/264690)

- Apr 27, 2021 (155)
21 ALFA NC_000018.10 - 9104681 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
82083620, ss5224114313 NC_000018.9:9104678:TCTC: NC_000018.10:9104680:TCTCTCTCTC:TC…

NC_000018.10:9104680:TCTCTCTCTC:TCTCTC

(self)
35961981, 114705235, ss3979583980, ss4317943683, ss5048328179, ss5780868131, ss5816856913, ss5873153576 NC_000018.10:9104680:TCTC: NC_000018.10:9104680:TCTCTCTCTC:TC…

NC_000018.10:9104680:TCTCTCTCTC:TCTCTC

(self)
4480511576 NC_000018.10:9104680:TCTCTCTCTC:TC…

NC_000018.10:9104680:TCTCTCTCTC:TCTCTC

NC_000018.10:9104680:TCTCTCTCTC:TC…

NC_000018.10:9104680:TCTCTCTCTC:TCTCTC

(self)
ss4317943682, ss5048328178 NC_000018.10:9104680:TC: NC_000018.10:9104680:TCTCTCTCTC:TC…

NC_000018.10:9104680:TCTCTCTCTC:TCTCTCTC

(self)
4480511576 NC_000018.10:9104680:TCTCTCTCTC:TC…

NC_000018.10:9104680:TCTCTCTCTC:TCTCTCTC

NC_000018.10:9104680:TCTCTCTCTC:TC…

NC_000018.10:9104680:TCTCTCTCTC:TCTCTCTC

(self)
ss4317943681, ss5048328177 NC_000018.10:9104680::TC NC_000018.10:9104680:TCTCTCTCTC:TC…

NC_000018.10:9104680:TCTCTCTCTC:TCTCTCTCTCTC

(self)
4480511576 NC_000018.10:9104680:TCTCTCTCTC:TC…

NC_000018.10:9104680:TCTCTCTCTC:TCTCTCTCTCTC

NC_000018.10:9104680:TCTCTCTCTC:TC…

NC_000018.10:9104680:TCTCTCTCTC:TCTCTCTCTCTC

(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 rs1369955901

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