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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.

rs1374726893

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:48298509 (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
G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000007 (1/140236, GnomAD)
C=0.00007 (1/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NME6 : Stop Gained
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 14050 G=0.99993 C=0.00007 0.999858 0.0 0.000142 0
European Sub 9690 G=0.9999 C=0.0001 0.999794 0.0 0.000206 0
African Sub 2898 G=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 G=1.000 C=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 G=1.0000 C=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 G=1.000 C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 G=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 G=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 C=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 G=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Sub 496 G=1.000 C=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
gnomAD - Genomes Global Study-wide 140236 G=0.999993 C=0.000007
gnomAD - Genomes European Sub 75934 G=0.99999 C=0.00001
gnomAD - Genomes African Sub 42044 G=1.00000 C=0.00000
gnomAD - Genomes American Sub 13648 G=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2152 G=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 14050 G=0.99993 C=0.00007
Allele Frequency Aggregator European Sub 9690 G=0.9999 C=0.0001
Allele Frequency Aggregator African Sub 2898 G=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 C=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 C=0.00
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 3 NC_000003.12:g.48298509G>C
GRCh37.p13 chr 3 NC_000003.11:g.48339999G>C
Gene: NME6, NME/NM23 nucleoside diphosphate kinase 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NME6 transcript variant 8 NM_001308434.2:c.-45-1680…

NM_001308434.2:c.-45-1680C>G

N/A Intron Variant
NME6 transcript variant 2 NM_001308426.2:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform 2 NP_001295355.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant 9 NM_001308435.2:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform 6 NP_001295364.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant 6 NM_001308431.2:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform 4 NP_001295360.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant 4 NM_001308428.2:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform 2 NP_001295357.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant 7 NM_001308433.2:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform 4 NP_001295362.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant 1 NM_005793.5:c.32C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform 1 NP_005784.1:p.Ser11Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant 5 NM_001308430.2:c.32C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform 3 NP_001295359.1:p.Ser11Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant 3 NM_001308427.2:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform 2 NP_001295356.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X17 XM_017005517.2:c.17+2787C…

XM_017005517.2:c.17+2787C>G

N/A Intron Variant
NME6 transcript variant X1 XM_024453297.2:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X1 XP_024309065.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X2 XM_047447173.1:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X2 XP_047303129.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X3 XM_047447174.1:c.20C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X3 XP_047303130.1:p.Ser7Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X4 XM_024453299.2:c.140C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X4 XP_024309067.1:p.Ser47Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X5 XM_047447175.1:c.20C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X5 XP_047303131.1:p.Ser7Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X6 XM_024453300.2:c.32C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X6 XP_024309068.1:p.Ser11Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X7 XM_024453301.2:c.20C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X3 XP_024309069.1:p.Ser7Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X8 XM_024453302.2:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X1 XP_024309070.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X9 XM_024453303.2:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X1 XP_024309071.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X10 XM_047447176.1:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X1 XP_047303132.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X11 XM_047447177.1:c.140C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X7 XP_047303133.1:p.Ser47Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X12 XM_047447178.1:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X2 XP_047303134.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X13 XM_017005515.2:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X8 XP_016861004.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X14 XM_047447179.1:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X8 XP_047303135.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X15 XM_024453306.2:c.8C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X1 XP_024309074.1:p.Ser3Ter S (Ser) > * (Ter) Stop Gained
NME6 transcript variant X16 XM_017005516.3:c.32C>G S [TCA] > * [TGA] Coding Sequence Variant
nucleoside diphosphate kinase 6 isoform X9 XP_016861005.1:p.Ser11Ter S (Ser) > * (Ter) Stop Gained
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 G= C
GRCh38.p14 chr 3 NC_000003.12:g.48298509= NC_000003.12:g.48298509G>C
GRCh37.p13 chr 3 NC_000003.11:g.48339999= NC_000003.11:g.48339999G>C
NME6 transcript variant 1 NM_005793.5:c.32= NM_005793.5:c.32C>G
NME6 transcript variant 1 NM_005793.4:c.32= NM_005793.4:c.32C>G
NME6 transcript NM_005793.3:c.32= NM_005793.3:c.32C>G
NME6 transcript variant X16 XM_017005516.3:c.32= XM_017005516.3:c.32C>G
NME6 transcript variant X16 XM_017005516.2:c.32= XM_017005516.2:c.32C>G
NME6 transcript variant X6 XM_017005516.1:c.32= XM_017005516.1:c.32C>G
NME6 transcript variant 3 NM_001308427.2:c.8= NM_001308427.2:c.8C>G
NME6 transcript variant 3 NM_001308427.1:c.8= NM_001308427.1:c.8C>G
NME6 transcript variant 4 NM_001308428.2:c.8= NM_001308428.2:c.8C>G
NME6 transcript variant 4 NM_001308428.1:c.8= NM_001308428.1:c.8C>G
NME6 transcript variant X13 XM_017005515.2:c.8= XM_017005515.2:c.8C>G
NME6 transcript variant X14 XM_017005515.1:c.8= XM_017005515.1:c.8C>G
NME6 transcript variant 7 NM_001308433.2:c.8= NM_001308433.2:c.8C>G
NME6 transcript variant 7 NM_001308433.1:c.8= NM_001308433.1:c.8C>G
NME6 transcript variant 5 NM_001308430.2:c.32= NM_001308430.2:c.32C>G
NME6 transcript variant 5 NM_001308430.1:c.32= NM_001308430.1:c.32C>G
NME6 transcript variant 2 NM_001308426.2:c.8= NM_001308426.2:c.8C>G
NME6 transcript variant 2 NM_001308426.1:c.8= NM_001308426.1:c.8C>G
NME6 transcript variant 6 NM_001308431.2:c.8= NM_001308431.2:c.8C>G
NME6 transcript variant 6 NM_001308431.1:c.8= NM_001308431.1:c.8C>G
NME6 transcript variant 9 NM_001308435.2:c.8= NM_001308435.2:c.8C>G
NME6 transcript variant 9 NM_001308435.1:c.8= NM_001308435.1:c.8C>G
NME6 transcript variant X15 XM_024453306.2:c.8= XM_024453306.2:c.8C>G
NME6 transcript variant X15 XM_024453306.1:c.8= XM_024453306.1:c.8C>G
NME6 transcript variant X4 XM_024453299.2:c.140= XM_024453299.2:c.140C>G
NME6 transcript variant X3 XM_024453299.1:c.140= XM_024453299.1:c.140C>G
NME6 transcript variant X7 XM_024453301.2:c.20= XM_024453301.2:c.20C>G
NME6 transcript variant X7 XM_024453301.1:c.20= XM_024453301.1:c.20C>G
NME6 transcript variant X9 XM_024453303.2:c.8= XM_024453303.2:c.8C>G
NME6 transcript variant X9 XM_024453303.1:c.8= XM_024453303.1:c.8C>G
NME6 transcript variant X8 XM_024453302.2:c.8= XM_024453302.2:c.8C>G
NME6 transcript variant X8 XM_024453302.1:c.8= XM_024453302.1:c.8C>G
NME6 transcript variant X6 XM_024453300.2:c.32= XM_024453300.2:c.32C>G
NME6 transcript variant X5 XM_024453300.1:c.32= XM_024453300.1:c.32C>G
NME6 transcript variant X1 XM_024453297.2:c.8= XM_024453297.2:c.8C>G
NME6 transcript variant X1 XM_024453297.1:c.8= XM_024453297.1:c.8C>G
NME6 transcript variant X12 XM_047447178.1:c.8= XM_047447178.1:c.8C>G
NME6 transcript variant X11 XM_047447177.1:c.140= XM_047447177.1:c.140C>G
NME6 transcript variant X14 XM_047447179.1:c.8= XM_047447179.1:c.8C>G
NME6 transcript variant X2 XM_047447173.1:c.8= XM_047447173.1:c.8C>G
NME6 transcript variant X5 XM_047447175.1:c.20= XM_047447175.1:c.20C>G
NME6 transcript variant X10 XM_047447176.1:c.8= XM_047447176.1:c.8C>G
NME6 transcript variant X3 XM_047447174.1:c.20= XM_047447174.1:c.20C>G
nucleoside diphosphate kinase 6 isoform 1 NP_005784.1:p.Ser11= NP_005784.1:p.Ser11Ter
nucleoside diphosphate kinase 6 isoform X9 XP_016861005.1:p.Ser11= XP_016861005.1:p.Ser11Ter
nucleoside diphosphate kinase 6 isoform 2 NP_001295356.1:p.Ser3= NP_001295356.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform 2 NP_001295357.1:p.Ser3= NP_001295357.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform X8 XP_016861004.1:p.Ser3= XP_016861004.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform 4 NP_001295362.1:p.Ser3= NP_001295362.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform 3 NP_001295359.1:p.Ser11= NP_001295359.1:p.Ser11Ter
nucleoside diphosphate kinase 6 isoform 2 NP_001295355.1:p.Ser3= NP_001295355.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform 4 NP_001295360.1:p.Ser3= NP_001295360.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform 6 NP_001295364.1:p.Ser3= NP_001295364.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform X1 XP_024309074.1:p.Ser3= XP_024309074.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform X4 XP_024309067.1:p.Ser47= XP_024309067.1:p.Ser47Ter
nucleoside diphosphate kinase 6 isoform X3 XP_024309069.1:p.Ser7= XP_024309069.1:p.Ser7Ter
nucleoside diphosphate kinase 6 isoform X1 XP_024309071.1:p.Ser3= XP_024309071.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform X1 XP_024309070.1:p.Ser3= XP_024309070.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform X6 XP_024309068.1:p.Ser11= XP_024309068.1:p.Ser11Ter
nucleoside diphosphate kinase 6 isoform X1 XP_024309065.1:p.Ser3= XP_024309065.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform X2 XP_047303134.1:p.Ser3= XP_047303134.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform X7 XP_047303133.1:p.Ser47= XP_047303133.1:p.Ser47Ter
nucleoside diphosphate kinase 6 isoform X8 XP_047303135.1:p.Ser3= XP_047303135.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform X2 XP_047303129.1:p.Ser3= XP_047303129.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform X5 XP_047303131.1:p.Ser7= XP_047303131.1:p.Ser7Ter
nucleoside diphosphate kinase 6 isoform X1 XP_047303132.1:p.Ser3= XP_047303132.1:p.Ser3Ter
nucleoside diphosphate kinase 6 isoform X3 XP_047303130.1:p.Ser7= XP_047303130.1:p.Ser7Ter
NME6 transcript variant 8 NM_001308434.2:c.-45-1680= NM_001308434.2:c.-45-1680C>G
NME6 transcript variant X17 XM_017005517.2:c.17+2787= XM_017005517.2:c.17+2787C>G
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#.

2 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2746998490 Nov 08, 2017 (151)
2 GNOMAD ss2792564665 Nov 08, 2017 (151)
3 gnomAD - Genomes NC_000003.12 - 48298509 Apr 26, 2021 (155)
4 ALFA NC_000003.12 - 48298509 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
ss2746998490, ss2792564665 NC_000003.11:48339998:G:C NC_000003.12:48298508:G:C (self)
106784326, 11835792743 NC_000003.12:48298508:G:C NC_000003.12:48298508: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.

No publications for rs1374726893

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