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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 Aliases 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.

rs199883290

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr16:50729867 (GRCh38.p12) 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>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00000 (1/251370, GnomAD_exome)
C=0.00002 (2/125568, TOPMED)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NOD2 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
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.p12 chr 16 NC_000016.10:g.50729867G>A
GRCh38.p12 chr 16 NC_000016.10:g.50729867G>C
GRCh37.p13 chr 16 NC_000016.9:g.50763778G>A
GRCh37.p13 chr 16 NC_000016.9:g.50763778G>C
NOD2 RefSeqGene (LRG_177) NG_007508.1:g.37729G>A
NOD2 RefSeqGene (LRG_177) NG_007508.1:g.37729G>C
Gene: NOD2, nucleotide binding oligomerization domain containing 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NOD2 transcript variant 1 NM_022162.3:c.3016G>A A [GCC] > T [ACC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 1 NP_071445.1:p.Ala1006Thr A (Ala) > T (Thr) Missense Variant
NOD2 transcript variant 1 NM_022162.3:c.3016G>C A [GCC] > P [CCC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 1 NP_071445.1:p.Ala1006Pro A (Ala) > P (Pro) Missense Variant
NOD2 transcript variant 2 NM_001293557.2:c.2935G>A A [GCC] > T [ACC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001280486.1:p.Ala979Thr A (Ala) > T (Thr) Missense Variant
NOD2 transcript variant 2 NM_001293557.2:c.2935G>C A [GCC] > P [CCC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001280486.1:p.Ala979Pro A (Ala) > P (Pro) Missense Variant
NOD2 transcript variant 3 NM_001370466.1:c.2935G>A A [GCC] > T [ACC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001357395.1:p.Ala979Thr A (Ala) > T (Thr) Missense Variant
NOD2 transcript variant 3 NM_001370466.1:c.2935G>C A [GCC] > P [CCC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001357395.1:p.Ala979Pro A (Ala) > P (Pro) Missense Variant
NOD2 transcript variant 4 NR_163434.1:n.3147G>A N/A Non Coding Transcript Variant
NOD2 transcript variant 4 NR_163434.1:n.3147G>C N/A Non Coding Transcript Variant
NOD2 transcript variant X9 XM_006721243.4:c. N/A Genic Downstream Transcript Variant
NOD2 transcript variant X10 XM_011523260.3:c. N/A Genic Downstream Transcript Variant
NOD2 transcript variant X12 XM_011523261.2:c. N/A Genic Downstream Transcript Variant
NOD2 transcript variant X3 XM_017023535.1:c.2443G>A A [GCC] > T [ACC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X3 XP_016879024.1:p.Ala815Thr A (Ala) > T (Thr) Missense Variant
NOD2 transcript variant X3 XM_017023535.1:c.2443G>C A [GCC] > P [CCC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X3 XP_016879024.1:p.Ala815Pro A (Ala) > P (Pro) Missense Variant
NOD2 transcript variant X4 XM_017023536.1:c.2350G>A A [GCC] > T [ACC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879025.1:p.Ala784Thr A (Ala) > T (Thr) Missense Variant
NOD2 transcript variant X4 XM_017023536.1:c.2350G>C A [GCC] > P [CCC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879025.1:p.Ala784Pro A (Ala) > P (Pro) Missense Variant
NOD2 transcript variant X5 XM_011523259.2:c.2350G>A A [GCC] > T [ACC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_011521561.1:p.Ala784Thr A (Ala) > T (Thr) Missense Variant
NOD2 transcript variant X5 XM_011523259.2:c.2350G>C A [GCC] > P [CCC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_011521561.1:p.Ala784Pro A (Ala) > P (Pro) Missense Variant
NOD2 transcript variant X6 XM_017023537.1:c.2350G>A A [GCC] > T [ACC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879026.1:p.Ala784Thr A (Ala) > T (Thr) Missense Variant
NOD2 transcript variant X6 XM_017023537.1:c.2350G>C A [GCC] > P [CCC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879026.1:p.Ala784Pro A (Ala) > P (Pro) Missense Variant
NOD2 transcript variant X13 XM_017023538.1:c.2350G>A A [GCC] > T [ACC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879027.1:p.Ala784Thr A (Ala) > T (Thr) Missense Variant
NOD2 transcript variant X13 XM_017023538.1:c.2350G>C A [GCC] > P [CCC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879027.1:p.Ala784Pro A (Ala) > P (Pro) Missense Variant
NOD2 transcript variant X2 XM_006721242.4:c.2851G>A A [GCC] > T [ACC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X2 XP_006721305.1:p.Ala951Thr A (Ala) > T (Thr) Missense Variant
NOD2 transcript variant X2 XM_006721242.4:c.2851G>C A [GCC] > P [CCC] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X2 XP_006721305.1:p.Ala951Pro A (Ala) > P (Pro) Missense Variant
NOD2 transcript variant X8 XR_429725.3:n. N/A Genic Downstream Transcript Variant
NOD2 transcript variant X11 XR_429726.3:n. N/A Genic Downstream Transcript Variant
NOD2 transcript variant X7 XR_933387.2:n. 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

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 251370 G=1.00000 A=0.00000
gnomAD - Exomes European Sub 135328 G=0.99999 A=0.00001
gnomAD - Exomes Asian Sub 49004 G=1.0000 A=0.0000
gnomAD - Exomes American Sub 34572 G=1.0000 A=0.0000
gnomAD - Exomes African Sub 16254 G=1.0000 A=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 10074 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 6138 G=1.000 A=0.000
TopMed Global Study-wide 125568 G=0.99998 C=0.00002
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= A C Note
GRCh38.p12 chr 16 NC_000016.10:g.50...

NC_000016.10:g.50729867=

NC_000016.10:g.50...

NC_000016.10:g.50729867G>A

NC_000016.10:g.50...

NC_000016.10:g.50729867G>C

GRCh37.p13 chr 16 NC_000016.9:g.507...

NC_000016.9:g.50763778=

NC_000016.9:g.507...

NC_000016.9:g.50763778G>A

NC_000016.9:g.507...

NC_000016.9:g.50763778G>C

NOD2 RefSeqGene (LRG_177) NG_007508.1:g.37729= NG_007508.1:g.377...

NG_007508.1:g.37729G>A

NG_007508.1:g.377...

NG_007508.1:g.37729G>C

NOD2 transcript variant 1 NM_022162.3:c.3016= NM_022162.3:c.301...

NM_022162.3:c.3016G>A

NM_022162.3:c.301...

NM_022162.3:c.3016G>C

NOD2 transcript variant 1 NM_022162.2:c.3016= NM_022162.2:c.301...

NM_022162.2:c.3016G>A

NM_022162.2:c.301...

NM_022162.2:c.3016G>C

NOD2 transcript NM_022162.1:c.3016= NM_022162.1:c.301...

NM_022162.1:c.3016G>A

NM_022162.1:c.301...

NM_022162.1:c.3016G>C

NOD2 transcript variant 2 NM_001293557.2:c....

NM_001293557.2:c.2935=

NM_001293557.2:c....

NM_001293557.2:c.2935G>A

NM_001293557.2:c....

NM_001293557.2:c.2935G>C

NOD2 transcript variant 2 NM_001293557.1:c....

NM_001293557.1:c.2935=

NM_001293557.1:c....

NM_001293557.1:c.2935G>A

NM_001293557.1:c....

NM_001293557.1:c.2935G>C

NOD2 transcript variant 4 NR_163434.1:n.3147= NR_163434.1:n.314...

NR_163434.1:n.3147G>A

NR_163434.1:n.314...

NR_163434.1:n.3147G>C

NOD2 transcript variant 3 NM_001370466.1:c....

NM_001370466.1:c.2935=

NM_001370466.1:c....

NM_001370466.1:c.2935G>A

NM_001370466.1:c....

NM_001370466.1:c.2935G>C

NOD2 transcript variant X2 XM_006721242.4:c....

XM_006721242.4:c.2851=

XM_006721242.4:c....

XM_006721242.4:c.2851G>A

XM_006721242.4:c....

XM_006721242.4:c.2851G>C

NOD2 transcript variant X5 XM_011523259.2:c....

XM_011523259.2:c.2350=

XM_011523259.2:c....

XM_011523259.2:c.2350G>A

XM_011523259.2:c....

XM_011523259.2:c.2350G>C

NOD2 transcript variant X3 XM_017023535.1:c....

XM_017023535.1:c.2443=

XM_017023535.1:c....

XM_017023535.1:c.2443G>A

XM_017023535.1:c....

XM_017023535.1:c.2443G>C

NOD2 transcript variant X4 XM_017023536.1:c....

XM_017023536.1:c.2350=

XM_017023536.1:c....

XM_017023536.1:c.2350G>A

XM_017023536.1:c....

XM_017023536.1:c.2350G>C

NOD2 transcript variant X13 XM_017023538.1:c....

XM_017023538.1:c.2350=

XM_017023538.1:c....

XM_017023538.1:c.2350G>A

XM_017023538.1:c....

XM_017023538.1:c.2350G>C

NOD2 transcript variant X6 XM_017023537.1:c....

XM_017023537.1:c.2350=

XM_017023537.1:c....

XM_017023537.1:c.2350G>A

XM_017023537.1:c....

XM_017023537.1:c.2350G>C

nucleotide-binding oligomerization domain-containing protein 2 isoform 1 NP_071445.1:p.Ala...

NP_071445.1:p.Ala1006=

NP_071445.1:p.Ala...

NP_071445.1:p.Ala1006Thr

NP_071445.1:p.Ala...

NP_071445.1:p.Ala1006Pro

nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001280486.1:p....

NP_001280486.1:p.Ala979=

NP_001280486.1:p....

NP_001280486.1:p.Ala979Thr

NP_001280486.1:p....

NP_001280486.1:p.Ala979Pro

nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001357395.1:p....

NP_001357395.1:p.Ala979=

NP_001357395.1:p....

NP_001357395.1:p.Ala979Thr

NP_001357395.1:p....

NP_001357395.1:p.Ala979Pro

nucleotide-binding oligomerization domain-containing protein 2 isoform X2 XP_006721305.1:p....

XP_006721305.1:p.Ala951=

XP_006721305.1:p....

XP_006721305.1:p.Ala951Thr

XP_006721305.1:p....

XP_006721305.1:p.Ala951Pro

nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_011521561.1:p....

XP_011521561.1:p.Ala784=

XP_011521561.1:p....

XP_011521561.1:p.Ala784Thr

XP_011521561.1:p....

XP_011521561.1:p.Ala784Pro

nucleotide-binding oligomerization domain-containing protein 2 isoform X3 XP_016879024.1:p....

XP_016879024.1:p.Ala815=

XP_016879024.1:p....

XP_016879024.1:p.Ala815Thr

XP_016879024.1:p....

XP_016879024.1:p.Ala815Pro

nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879025.1:p....

XP_016879025.1:p.Ala784=

XP_016879025.1:p....

XP_016879025.1:p.Ala784Thr

XP_016879025.1:p....

XP_016879025.1:p.Ala784Pro

nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879027.1:p....

XP_016879027.1:p.Ala784=

XP_016879027.1:p....

XP_016879027.1:p.Ala784Thr

XP_016879027.1:p....

XP_016879027.1:p.Ala784Pro

nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879026.1:p....

XP_016879026.1:p.Ala784=

XP_016879026.1:p....

XP_016879026.1:p.Ala784Thr

XP_016879026.1:p....

XP_016879026.1:p.Ala784Pro

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#.

3 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 EXOME_CHIP ss491508232 May 04, 2012 (137)
2 TOPMED ss2376991853 Dec 20, 2016 (150)
3 TOPMED ss3246277348 Nov 08, 2017 (151)
4 gnomAD - Exomes NC_000016.9 - 50763778 Jul 13, 2019 (153)
5 TopMed NC_000016.10 - 50729867 Oct 12, 2018 (152)
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
11255499 NC_000016.9:50763777:G:A NC_000016.10:50729866:G:A
ss491508232, ss2376991853 NC_000016.9:50763777:G:C NC_000016.10:50729866:G:C (self)
143973685, ss3246277348 NC_000016.10:50729866:G:C NC_000016.10:50729866: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 rs199883290

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.post308+0fe9b3b