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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1451493475

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:68158938 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
A=0.000008 (2/250818, GnomAD_exome)
A=0.00004 (1/23038, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KMT5B : Missense 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 23038 G=0.99996 A=0.00004 0.999913 0.0 8.7e-05 0
European Sub 15752 G=1.00000 A=0.00000 1.0 0.0 0.0 N/A
African Sub 3492 G=0.9997 A=0.0003 0.999427 0.0 0.000573 0
African Others Sub 122 G=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 3370 G=0.9997 A=0.0003 0.999407 0.0 0.000593 0
Asian Sub 168 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 112 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 56 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 2772 G=1.0000 A=0.0000 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
TopMed Global Study-wide 264690 G=0.999996 A=0.000004
gnomAD - Exomes Global Study-wide 250818 G=0.999992 A=0.000008
gnomAD - Exomes European Sub 135184 G=0.999993 A=0.000007
gnomAD - Exomes Asian Sub 48790 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34474 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16186 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10068 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6116 G=0.9998 A=0.0002
Allele Frequency Aggregator Total Global 23038 G=0.99996 A=0.00004
Allele Frequency Aggregator European Sub 15752 G=1.00000 A=0.00000
Allele Frequency Aggregator African Sub 3492 G=0.9997 A=0.0003
Allele Frequency Aggregator Other Sub 2772 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 168 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=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 11 NC_000011.10:g.68158938G>A
GRCh37.p13 chr 11 NC_000011.9:g.67926405G>A
KMT5B RefSeqGene NG_052873.1:g.59835C>T
Gene: KMT5B, lysine methyltransferase 5B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
KMT5B transcript variant 5 NM_001300909.2:c. N/A Genic Downstream Transcript Variant
KMT5B transcript variant 6 NM_001363566.2:c. N/A Genic Downstream Transcript Variant
KMT5B transcript variant 7 NM_001369424.1:c. N/A Genic Downstream Transcript Variant
KMT5B transcript variant 8 NM_001369425.1:c. N/A Genic Downstream Transcript Variant
KMT5B transcript variant 10 NM_001369427.1:c. N/A Genic Downstream Transcript Variant
KMT5B transcript variant 2 NM_016028.4:c. N/A Genic Downstream Transcript Variant
KMT5B transcript variant 3 NM_001300907.1:c.892C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001287836.1:p.Leu298Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant 1 NM_017635.5:c.1408C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform 1 NP_060105.3:p.Leu470Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant 13 NM_001369430.1:c.892C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356359.1:p.Leu298Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant 9 NM_001369426.1:c.1408C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform 1 NP_001356355.1:p.Leu470Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant 11 NM_001369428.1:c.892C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356357.1:p.Leu298Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant 16 NM_001369433.1:c.892C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356362.1:p.Leu298Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant 14 NM_001369431.1:c.892C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356360.1:p.Leu298Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant 12 NM_001369429.1:c.892C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356358.1:p.Leu298Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant 15 NM_001369432.1:c.892C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356361.1:p.Leu298Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant 4 NM_001300908.2:c.688C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform 4 NP_001287837.1:p.Leu230Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant 17 NR_161378.1:n. N/A Genic Downstream Transcript Variant
KMT5B transcript variant 18 NR_161379.1:n. N/A Genic Downstream Transcript Variant
KMT5B transcript variant 19 NR_161380.1:n. N/A Genic Downstream Transcript Variant
KMT5B transcript variant X4 XM_006718581.2:c.1339C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform X2 XP_006718644.1:p.Leu447Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant X1 XM_005274035.5:c.1408C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform X1 XP_005274092.2:p.Leu470Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant X2 XM_047427071.1:c.1408C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform X1 XP_047283027.1:p.Leu470Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant X3 XM_005274036.5:c.1339C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform X2 XP_005274093.2:p.Leu447Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant X5 XM_011545092.4:c.1195C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform X3 XP_011543394.1:p.Leu399Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant X6 XM_047427072.1:c.1126C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform X4 XP_047283028.1:p.Leu376Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant X7 XM_047427073.1:c.166C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform X5 XP_047283029.1:p.Leu56Phe L (Leu) > F (Phe) Missense Variant
KMT5B transcript variant X8 XM_024448570.2:c.166C>T L [CTC] > F [TTC] Coding Sequence Variant
histone-lysine N-methyltransferase KMT5B isoform X5 XP_024304338.1:p.Leu56Phe L (Leu) > F (Phe) Missense 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 G= A
GRCh38.p14 chr 11 NC_000011.10:g.68158938= NC_000011.10:g.68158938G>A
GRCh37.p13 chr 11 NC_000011.9:g.67926405= NC_000011.9:g.67926405G>A
KMT5B RefSeqGene NG_052873.1:g.59835= NG_052873.1:g.59835C>T
KMT5B transcript variant 1 NM_017635.5:c.1408= NM_017635.5:c.1408C>T
KMT5B transcript variant 1 NM_017635.4:c.1408= NM_017635.4:c.1408C>T
SUV420H1 transcript variant 1 NM_017635.3:c.1408= NM_017635.3:c.1408C>T
KMT5B transcript variant 4 NM_001300908.2:c.688= NM_001300908.2:c.688C>T
KMT5B transcript variant 4 NM_001300908.1:c.688= NM_001300908.1:c.688C>T
KMT5B transcript variant 16 NM_001369433.1:c.892= NM_001369433.1:c.892C>T
KMT5B transcript variant 11 NM_001369428.1:c.892= NM_001369428.1:c.892C>T
KMT5B transcript variant 15 NM_001369432.1:c.892= NM_001369432.1:c.892C>T
KMT5B transcript variant 14 NM_001369431.1:c.892= NM_001369431.1:c.892C>T
KMT5B transcript variant 3 NM_001300907.1:c.892= NM_001300907.1:c.892C>T
KMT5B transcript variant 9 NM_001369426.1:c.1408= NM_001369426.1:c.1408C>T
KMT5B transcript variant 13 NM_001369430.1:c.892= NM_001369430.1:c.892C>T
KMT5B transcript variant 12 NM_001369429.1:c.892= NM_001369429.1:c.892C>T
KMT5B transcript variant X1 XM_005274035.5:c.1408= XM_005274035.5:c.1408C>T
KMT5B transcript variant X1 XM_005274035.4:c.1408= XM_005274035.4:c.1408C>T
KMT5B transcript variant X1 XM_005274035.3:c.1408= XM_005274035.3:c.1408C>T
SUV420H1 transcript variant X1 XM_005274035.2:c.1408= XM_005274035.2:c.1408C>T
SUV420H1 transcript variant X1 XM_005274035.1:c.1408= XM_005274035.1:c.1408C>T
KMT5B transcript variant X3 XM_005274036.5:c.1339= XM_005274036.5:c.1339C>T
KMT5B transcript variant X2 XM_005274036.4:c.1339= XM_005274036.4:c.1339C>T
KMT5B transcript variant X3 XM_005274036.3:c.1339= XM_005274036.3:c.1339C>T
SUV420H1 transcript variant X3 XM_005274036.2:c.1339= XM_005274036.2:c.1339C>T
SUV420H1 transcript variant X2 XM_005274036.1:c.1339= XM_005274036.1:c.1339C>T
KMT5B transcript variant X5 XM_011545092.4:c.1195= XM_011545092.4:c.1195C>T
KMT5B transcript variant X4 XM_011545092.3:c.1195= XM_011545092.3:c.1195C>T
KMT5B transcript variant X5 XM_011545092.2:c.1195= XM_011545092.2:c.1195C>T
SUV420H1 transcript variant X5 XM_011545092.1:c.1195= XM_011545092.1:c.1195C>T
KMT5B transcript variant X4 XM_006718581.2:c.1339= XM_006718581.2:c.1339C>T
KMT5B transcript variant X4 XM_006718581.1:c.1339= XM_006718581.1:c.1339C>T
KMT5B transcript variant X8 XM_024448570.2:c.166= XM_024448570.2:c.166C>T
KMT5B transcript variant X9 XM_024448570.1:c.166= XM_024448570.1:c.166C>T
KMT5B transcript variant X2 XM_047427071.1:c.1408= XM_047427071.1:c.1408C>T
KMT5B transcript variant X6 XM_047427072.1:c.1126= XM_047427072.1:c.1126C>T
KMT5B transcript variant X7 XM_047427073.1:c.166= XM_047427073.1:c.166C>T
histone-lysine N-methyltransferase KMT5B isoform 1 NP_060105.3:p.Leu470= NP_060105.3:p.Leu470Phe
histone-lysine N-methyltransferase KMT5B isoform 4 NP_001287837.1:p.Leu230= NP_001287837.1:p.Leu230Phe
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356362.1:p.Leu298= NP_001356362.1:p.Leu298Phe
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356357.1:p.Leu298= NP_001356357.1:p.Leu298Phe
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356361.1:p.Leu298= NP_001356361.1:p.Leu298Phe
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356360.1:p.Leu298= NP_001356360.1:p.Leu298Phe
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001287836.1:p.Leu298= NP_001287836.1:p.Leu298Phe
histone-lysine N-methyltransferase KMT5B isoform 1 NP_001356355.1:p.Leu470= NP_001356355.1:p.Leu470Phe
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356359.1:p.Leu298= NP_001356359.1:p.Leu298Phe
histone-lysine N-methyltransferase KMT5B isoform 3 NP_001356358.1:p.Leu298= NP_001356358.1:p.Leu298Phe
histone-lysine N-methyltransferase KMT5B isoform X1 XP_005274092.2:p.Leu470= XP_005274092.2:p.Leu470Phe
histone-lysine N-methyltransferase KMT5B isoform X2 XP_005274093.2:p.Leu447= XP_005274093.2:p.Leu447Phe
histone-lysine N-methyltransferase KMT5B isoform X3 XP_011543394.1:p.Leu399= XP_011543394.1:p.Leu399Phe
histone-lysine N-methyltransferase KMT5B isoform X2 XP_006718644.1:p.Leu447= XP_006718644.1:p.Leu447Phe
histone-lysine N-methyltransferase KMT5B isoform X5 XP_024304338.1:p.Leu56= XP_024304338.1:p.Leu56Phe
histone-lysine N-methyltransferase KMT5B isoform X1 XP_047283027.1:p.Leu470= XP_047283027.1:p.Leu470Phe
histone-lysine N-methyltransferase KMT5B isoform X4 XP_047283028.1:p.Leu376= XP_047283028.1:p.Leu376Phe
histone-lysine N-methyltransferase KMT5B isoform X5 XP_047283029.1:p.Leu56= XP_047283029.1:p.Leu56Phe
histone-lysine N-methyltransferase SUV420H1 isoform X1 XP_005274092.1:p.Leu470= XP_005274092.1:p.Leu470Phe
histone-lysine N-methyltransferase SUV420H1 isoform X2 XP_005274093.1:p.Leu447= XP_005274093.1:p.Leu447Phe
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 GNOMAD ss2739194209 Nov 08, 2017 (151)
2 TOPMED ss4889041233 Apr 26, 2021 (155)
3 gnomAD - Exomes NC_000011.9 - 67926405 Jul 13, 2019 (153)
4 TopMed NC_000011.10 - 68158938 Apr 26, 2021 (155)
5 ALFA NC_000011.10 - 68158938 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
8409851, ss2739194209 NC_000011.9:67926404:G:A NC_000011.10:68158937:G:A (self)
104586889, 2372665124, ss4889041233 NC_000011.10:68158937:G:A NC_000011.10:68158937:G:A (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 rs1451493475

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