Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs752665647

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:26183815-26183816 (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
delC
Variation Type
Indel Insertion and Deletion
Frequency
delC=0.001417 (375/264690, TOPMED)
delC=0.001340 (337/251452, GnomAD_exome)
delC=0.001548 (217/140214, GnomAD) (+ 7 more)
delC=0.001327 (161/121368, ExAC)
delC=0.00160 (44/27508, ALFA)
delC=0.00224 (28/12518, GO-ESP)
delC=0.0005 (3/6404, 1000G_30x)
delC=0.0016 (7/4480, Estonian)
delC=0.0029 (11/3854, ALSPAC)
delC=0.0019 (7/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
H2BC6 : Frameshift 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 27508 CC=0.99840 C=0.00160
European Sub 20214 CC=0.99797 C=0.00203
African Sub 3492 CC=0.9997 C=0.0003
African Others Sub 122 CC=1.000 C=0.000
African American Sub 3370 CC=0.9997 C=0.0003
Asian Sub 168 CC=1.000 C=0.000
East Asian Sub 112 CC=1.000 C=0.000
Other Asian Sub 56 CC=1.00 C=0.00
Latin American 1 Sub 146 CC=1.000 C=0.000
Latin American 2 Sub 610 CC=1.000 C=0.000
South Asian Sub 98 CC=1.00 C=0.00
Other Sub 2780 CC=0.9993 C=0.0007


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 CC=0.998583 delC=0.001417
gnomAD - Exomes Global Study-wide 251452 CC=0.998660 delC=0.001340
gnomAD - Exomes European Sub 135396 CC=0.997710 delC=0.002290
gnomAD - Exomes Asian Sub 49010 CC=1.00000 delC=0.00000
gnomAD - Exomes American Sub 34586 CC=0.99971 delC=0.00029
gnomAD - Exomes African Sub 16254 CC=0.99945 delC=0.00055
gnomAD - Exomes Ashkenazi Jewish Sub 10076 CC=0.99990 delC=0.00010
gnomAD - Exomes Other Sub 6130 CC=0.9989 delC=0.0011
gnomAD - Genomes Global Study-wide 140214 CC=0.998452 delC=0.001548
gnomAD - Genomes European Sub 75942 CC=0.99743 delC=0.00257
gnomAD - Genomes African Sub 42026 CC=0.99964 delC=0.00036
gnomAD - Genomes American Sub 13644 CC=0.99963 delC=0.00037
gnomAD - Genomes Ashkenazi Jewish Sub 3322 CC=1.0000 delC=0.0000
gnomAD - Genomes East Asian Sub 3130 CC=1.0000 delC=0.0000
gnomAD - Genomes Other Sub 2150 CC=0.9991 delC=0.0009
ExAC Global Study-wide 121368 CC=0.998673 delC=0.001327
ExAC Europe Sub 73324 CC=0.99794 delC=0.00206
ExAC Asian Sub 25166 CC=1.00000 delC=0.00000
ExAC American Sub 11578 CC=0.99957 delC=0.00043
ExAC African Sub 10392 CC=0.99952 delC=0.00048
ExAC Other Sub 908 CC=1.000 delC=0.000
Allele Frequency Aggregator Total Global 27508 CC=0.99840 delC=0.00160
Allele Frequency Aggregator European Sub 20214 CC=0.99797 delC=0.00203
Allele Frequency Aggregator African Sub 3492 CC=0.9997 delC=0.0003
Allele Frequency Aggregator Other Sub 2780 CC=0.9993 delC=0.0007
Allele Frequency Aggregator Latin American 2 Sub 610 CC=1.000 delC=0.000
Allele Frequency Aggregator Asian Sub 168 CC=1.000 delC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 CC=1.000 delC=0.000
Allele Frequency Aggregator South Asian Sub 98 CC=1.00 delC=0.00
GO Exome Sequencing Project Global Study-wide 12518 CC=0.99776 delC=0.00224
GO Exome Sequencing Project European American Sub 8254 CC=0.9967 delC=0.0033
GO Exome Sequencing Project African American Sub 4264 CC=0.9998 delC=0.0002
1000Genomes_30x Global Study-wide 6404 CC=0.9995 delC=0.0005
1000Genomes_30x African Sub 1786 CC=1.0000 delC=0.0000
1000Genomes_30x Europe Sub 1266 CC=0.9976 delC=0.0024
1000Genomes_30x South Asian Sub 1202 CC=1.0000 delC=0.0000
1000Genomes_30x East Asian Sub 1170 CC=1.0000 delC=0.0000
1000Genomes_30x American Sub 980 CC=1.000 delC=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 CC=0.9984 delC=0.0016
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 CC=0.9971 delC=0.0029
UK 10K study - Twins TWIN COHORT Study-wide 3708 CC=0.9981 delC=0.0019
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 6 NC_000006.12:g.26183816del
GRCh37.p13 chr 6 NC_000006.11:g.26184044del
Gene: H2BC6, H2B clustered histone 6 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
H2BC6 transcript NM_003523.3:c.21del S [TCC] > S [TC] Coding Sequence Variant
histone H2B type 1-C/E/F/G/I NP_003514.2:p.Ala8fs S (Ser) > S (Ser) Frameshift 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 CC= delC
GRCh38.p14 chr 6 NC_000006.12:g.26183815_26183816= NC_000006.12:g.26183816del
GRCh37.p13 chr 6 NC_000006.11:g.26184043_26184044= NC_000006.11:g.26184044del
H2BC6 transcript NM_003523.3:c.20_21= NM_003523.3:c.21del
H2BC6 transcript NM_003523.2:c.20_21= NM_003523.2:c.21del
histone H2B type 1-C/E/F/G/I NP_003514.2:p.Ser7= NP_003514.2:p.Ala8fs
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#.

21 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_DECODE ss1592257740 Apr 01, 2015 (144)
2 EVA_UK10K_ALSPAC ss1705088597 Apr 01, 2015 (144)
3 EVA_UK10K_TWINSUK ss1705088598 Apr 01, 2015 (144)
4 EVA_EXAC ss1711814278 Apr 01, 2015 (144)
5 GNOMAD ss2735586258 Nov 08, 2017 (151)
6 GNOMAD ss2747561940 Nov 08, 2017 (151)
7 GNOMAD ss2837008030 Nov 08, 2017 (151)
8 SWEGEN ss2998702100 Nov 08, 2017 (151)
9 ILLUMINA ss3022585533 Nov 08, 2017 (151)
10 ILLUMINA ss3653095394 Oct 12, 2018 (152)
11 EGCUT_WGS ss3666634741 Jul 13, 2019 (153)
12 EVA_DECODE ss3716811982 Jul 13, 2019 (153)
13 ILLUMINA ss3726320206 Jul 13, 2019 (153)
14 EVA ss3824162224 Apr 26, 2020 (154)
15 TOPMED ss4697260246 Apr 26, 2021 (155)
16 1000G_HIGH_COVERAGE ss5267793008 Oct 13, 2022 (156)
17 HUGCELL_USP ss5465551297 Oct 13, 2022 (156)
18 1000G_HIGH_COVERAGE ss5553396000 Oct 13, 2022 (156)
19 EVA ss5841951625 Oct 13, 2022 (156)
20 EVA ss5848647497 Oct 13, 2022 (156)
21 EVA ss5968500783 Oct 13, 2022 (156)
22 1000Genomes_30x NC_000006.12 - 26183815 Oct 13, 2022 (156)
23 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 26184043 Oct 12, 2018 (152)
24 Genetic variation in the Estonian population NC_000006.11 - 26184043 Oct 12, 2018 (152)
25 ExAC NC_000006.11 - 26184043 Oct 12, 2018 (152)
26 gnomAD - Genomes NC_000006.12 - 26183815 Apr 26, 2021 (155)
27 gnomAD - Exomes NC_000006.11 - 26184043 Jul 13, 2019 (153)
28 GO Exome Sequencing Project NC_000006.11 - 26184043 Oct 12, 2018 (152)
29 TopMed NC_000006.12 - 26183815 Apr 26, 2021 (155)
30 UK 10K study - Twins NC_000006.11 - 26184043 Oct 12, 2018 (152)
31 ALFA NC_000006.12 - 26183815 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
ss1592257740 NC_000006.10:26292021:C: NC_000006.12:26183814:CC:C (self)
17370640, 12372989, 8210763, 4725993, 620263, 17370640, ss1705088597, ss1705088598, ss1711814278, ss2735586258, ss2747561940, ss2837008030, ss2998702100, ss3022585533, ss3653095394, ss3666634741, ss3824162224, ss5841951625, ss5968500783 NC_000006.11:26184042:C: NC_000006.12:26183814:CC:C (self)
ss5848647497 NC_000006.11:26184043:C: NC_000006.12:26183814:CC:C
40921935, 220201155, 534637804, ss3716811982, ss3726320206, ss4697260246, ss5267793008, ss5465551297, ss5553396000 NC_000006.12:26183814:C: NC_000006.12:26183814:CC:C (self)
8021190046 NC_000006.12:26183814:CC:C NC_000006.12:26183814:CC: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 rs752665647

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.post761+d5e8e07