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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.

rs781755968

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr16:15724743 (GRCh38.p13) 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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000014 (2/140258, GnomAD)
T=0.000008 (1/121374, ExAC)
T=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MYH11 : Synonymous Variant
NDE1 : 3 Prime UTR 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.p13 chr 16 NC_000016.10:g.15724743C>T
GRCh37.p13 chr 16 NC_000016.9:g.15818600C>T
MYH11 RefSeqGene (LRG_1401) NG_009299.1:g.137288G>A
NDE1 RefSeqGene NG_021210.1:g.86477C>T
GRCh38.p13 chr 16 alt locus HSCHR16_1_CTG1 NT_187607.1:g.1382754C>T
Gene: NDE1, nudE neurodevelopment protein 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NDE1 transcript variant 2 NM_017668.3:c.*492= N/A 3 Prime UTR Variant
NDE1 transcript variant 1 NM_001143979.2:c.*492= N/A 3 Prime UTR Variant
NDE1 transcript variant X1 XM_005255396.5:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X6 XM_006720897.4:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X10 XM_006720900.4:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X11 XM_011522553.2:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X2 XM_017023349.2:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X3 XM_017023350.1:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X4 XM_017023351.2:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X5 XM_017023352.2:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X7 XM_017023353.2:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X8 XM_017023354.2:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X9 XM_017023355.2:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X12 XM_017023356.2:c. N/A Genic Downstream Transcript Variant
NDE1 transcript variant X13 XM_017023357.2:c. N/A Genic Downstream Transcript Variant
Gene: MYH11, myosin heavy chain 11 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MYH11 transcript variant SM1A NM_002474.3:c.4020G>A Q [CAG] > Q [CAA] Coding Sequence Variant
myosin-11 isoform SM1A NP_002465.1:p.Gln1340= Q (Gln) > Q (Gln) Synonymous Variant
MYH11 transcript variant SM2B NM_001040113.2:c.4041G>A Q [CAG] > Q [CAA] Coding Sequence Variant
myosin-11 isoform SM2B NP_001035202.1:p.Gln1347= Q (Gln) > Q (Gln) Synonymous Variant
MYH11 transcript variant SM2A NM_022844.3:c.4020G>A Q [CAG] > Q [CAA] Coding Sequence Variant
myosin-11 isoform SM2A NP_074035.1:p.Gln1340= Q (Gln) > Q (Gln) Synonymous Variant
MYH11 transcript variant SM1B NM_001040114.2:c.4041G>A Q [CAG] > Q [CAA] Coding Sequence Variant
myosin-11 isoform SM1B NP_001035203.1:p.Gln1347= Q (Gln) > Q (Gln) Synonymous Variant
MYH11 transcript variant X1 XM_017023250.1:c.4041G>A Q [CAG] > Q [CAA] Coding Sequence Variant
myosin-11 isoform X1 XP_016878739.1:p.Gln1347= Q (Gln) > Q (Gln) Synonymous Variant
MYH11 transcript variant X2 XM_011522502.2:c.4020G>A Q [CAG] > Q [CAA] Coding Sequence Variant
myosin-11 isoform X2 XP_011520804.1:p.Gln1340= Q (Gln) > Q (Gln) Synonymous 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 10680 C=1.00000 T=0.00000
European Sub 6962 C=1.0000 T=0.0000
African Sub 2294 C=1.0000 T=0.0000
African Others Sub 84 C=1.00 T=0.00
African American Sub 2210 C=1.0000 T=0.0000
Asian Sub 108 C=1.000 T=0.000
East Asian Sub 84 C=1.00 T=0.00
Other Asian Sub 24 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 94 C=1.00 T=0.00
Other Sub 466 C=1.000 T=0.000


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 140258 C=0.999986 T=0.000014
gnomAD - Genomes European Sub 75944 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 42052 C=0.99995 T=0.00005
gnomAD - Genomes American Sub 13652 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
ExAC Global Study-wide 121374 C=0.999992 T=0.000008
ExAC Europe Sub 73330 C=1.00000 T=0.00000
ExAC Asian Sub 25162 C=1.00000 T=0.00000
ExAC American Sub 11574 C=1.00000 T=0.00000
ExAC African Sub 10400 C=0.99990 T=0.00010
ExAC Other Sub 908 C=1.000 T=0.000
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 C= T
GRCh38.p13 chr 16 NC_000016.10:g.15724743= NC_000016.10:g.15724743C>T
GRCh37.p13 chr 16 NC_000016.9:g.15818600= NC_000016.9:g.15818600C>T
MYH11 RefSeqGene (LRG_1401) NG_009299.1:g.137288= NG_009299.1:g.137288G>A
MYH11 transcript variant SM2A NM_022844.3:c.4020= NM_022844.3:c.4020G>A
MYH11 transcript variant SM2A NM_022844.2:c.4020= NM_022844.2:c.4020G>A
MYH11 transcript variant SM1A NM_002474.3:c.4020= NM_002474.3:c.4020G>A
MYH11 transcript variant SM1A NM_002474.2:c.4020= NM_002474.2:c.4020G>A
MYH11 transcript variant SM2B NM_001040113.2:c.4041= NM_001040113.2:c.4041G>A
MYH11 transcript variant SM2B NM_001040113.1:c.4041= NM_001040113.1:c.4041G>A
MYH11 transcript variant SM1B NM_001040114.2:c.4041= NM_001040114.2:c.4041G>A
MYH11 transcript variant SM1B NM_001040114.1:c.4041= NM_001040114.1:c.4041G>A
NDE1 RefSeqGene NG_021210.1:g.86477= NG_021210.1:g.86477C>T
NDE1 transcript variant 2 NM_017668.3:c.*492= NM_017668.3:c.*492C>T
NDE1 transcript variant 2 NM_017668.2:c.*492= NM_017668.2:c.*492C>T
NDE1 transcript variant 1 NM_001143979.2:c.*492= NM_001143979.2:c.*492C>T
NDE1 transcript variant 1 NM_001143979.1:c.*492= NM_001143979.1:c.*492C>T
GRCh38.p13 chr 16 alt locus HSCHR16_1_CTG1 NT_187607.1:g.1382754= NT_187607.1:g.1382754C>T
MYH11 transcript variant X2 XM_011522502.2:c.4020= XM_011522502.2:c.4020G>A
MYH11 transcript variant X1 XM_017023250.1:c.4041= XM_017023250.1:c.4041G>A
myosin-11 isoform SM2A NP_074035.1:p.Gln1340= NP_074035.1:p.Gln1340=
myosin-11 isoform SM1A NP_002465.1:p.Gln1340= NP_002465.1:p.Gln1340=
myosin-11 isoform SM2B NP_001035202.1:p.Gln1347= NP_001035202.1:p.Gln1347=
myosin-11 isoform SM1B NP_001035203.1:p.Gln1347= NP_001035203.1:p.Gln1347=
myosin-11 isoform X2 XP_011520804.1:p.Gln1340= XP_011520804.1:p.Gln1340=
myosin-11 isoform X1 XP_016878739.1:p.Gln1347= XP_016878739.1:p.Gln1347=
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, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1692174301 Apr 01, 2015 (144)
2 GNOMAD ss4297733932 Apr 26, 2021 (155)
3 ExAC NC_000016.9 - 15818600 Oct 12, 2018 (152)
4 gnomAD - Genomes NC_000016.10 - 15724743 Apr 26, 2021 (155)
5 ALFA NC_000016.10 - 15724743 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
2572520, ss1692174301 NC_000016.9:15818599:C:T NC_000016.10:15724742:C:T (self)
484289768, 3691061189, ss4297733932 NC_000016.10:15724742:C:T NC_000016.10:15724742:C:T
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 rs781755968

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.post596+ae089ad