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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.

rs16926398

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:60694186 (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=0.123050 (32570/264690, TOPMED)
A=0.119720 (16783/140186, GnomAD)
A=0.06247 (2913/46632, ALFA) (+ 18 more)
A=0.00619 (175/28258, 14KJPN)
A=0.00615 (103/16760, 8.3KJPN)
A=0.1304 (835/6404, 1000G_30x)
A=0.1264 (633/5008, 1000G)
A=0.0371 (166/4480, Estonian)
A=0.0288 (111/3854, ALSPAC)
A=0.0340 (126/3708, TWINSUK)
A=0.0007 (2/2922, KOREAN)
A=0.0033 (6/1832, Korea1K)
A=0.025 (25/998, GoNL)
A=0.027 (16/600, NorthernSweden)
A=0.159 (52/328, HapMap)
A=0.097 (21/216, Qatari)
A=0.019 (4/216, Vietnamese)
G=0.42 (34/80, SGDP_PRJ)
A=0.05 (2/40, GENOME_DK)
G=0.5 (3/6, Siberian)
A=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CHD7 : Intron 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 46632 G=0.93753 A=0.06247
European Sub 32396 G=0.96780 A=0.03220
African Sub 4936 G=0.6957 A=0.3043
African Others Sub 180 G=0.678 A=0.322
African American Sub 4756 G=0.6964 A=0.3036
Asian Sub 438 G=0.986 A=0.014
East Asian Sub 372 G=0.992 A=0.008
Other Asian Sub 66 G=0.95 A=0.05
Latin American 1 Sub 574 G=0.909 A=0.091
Latin American 2 Sub 4880 G=0.9734 A=0.0266
South Asian Sub 162 G=0.895 A=0.105
Other Sub 3246 G=0.9498 A=0.0502


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=0.876950 A=0.123050
gnomAD - Genomes Global Study-wide 140186 G=0.880280 A=0.119720
gnomAD - Genomes European Sub 75944 G=0.96825 A=0.03175
gnomAD - Genomes African Sub 41972 G=0.68396 A=0.31604
gnomAD - Genomes American Sub 13660 G=0.94575 A=0.05425
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9603 A=0.0397
gnomAD - Genomes East Asian Sub 3132 G=0.9917 A=0.0083
gnomAD - Genomes Other Sub 2154 G=0.9034 A=0.0966
Allele Frequency Aggregator Total Global 46632 G=0.93753 A=0.06247
Allele Frequency Aggregator European Sub 32396 G=0.96780 A=0.03220
Allele Frequency Aggregator African Sub 4936 G=0.6957 A=0.3043
Allele Frequency Aggregator Latin American 2 Sub 4880 G=0.9734 A=0.0266
Allele Frequency Aggregator Other Sub 3246 G=0.9498 A=0.0502
Allele Frequency Aggregator Latin American 1 Sub 574 G=0.909 A=0.091
Allele Frequency Aggregator Asian Sub 438 G=0.986 A=0.014
Allele Frequency Aggregator South Asian Sub 162 G=0.895 A=0.105
14KJPN JAPANESE Study-wide 28258 G=0.99381 A=0.00619
8.3KJPN JAPANESE Study-wide 16760 G=0.99385 A=0.00615
1000Genomes_30x Global Study-wide 6404 G=0.8696 A=0.1304
1000Genomes_30x African Sub 1786 G=0.6456 A=0.3544
1000Genomes_30x Europe Sub 1266 G=0.9724 A=0.0276
1000Genomes_30x South Asian Sub 1202 G=0.9151 A=0.0849
1000Genomes_30x East Asian Sub 1170 G=0.9932 A=0.0068
1000Genomes_30x American Sub 980 G=0.942 A=0.058
1000Genomes Global Study-wide 5008 G=0.8736 A=0.1264
1000Genomes African Sub 1322 G=0.6460 A=0.3540
1000Genomes East Asian Sub 1008 G=0.9931 A=0.0069
1000Genomes Europe Sub 1006 G=0.9702 A=0.0298
1000Genomes South Asian Sub 978 G=0.912 A=0.088
1000Genomes American Sub 694 G=0.939 A=0.061
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9629 A=0.0371
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9712 A=0.0288
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9660 A=0.0340
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9993 A=0.0007
Korean Genome Project KOREAN Study-wide 1832 G=0.9967 A=0.0033
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.975 A=0.025
Northern Sweden ACPOP Study-wide 600 G=0.973 A=0.027
HapMap Global Study-wide 328 G=0.841 A=0.159
HapMap African Sub 120 G=0.592 A=0.408
HapMap American Sub 118 G=0.975 A=0.025
HapMap Asian Sub 90 G=1.00 A=0.00
Qatari Global Study-wide 216 G=0.903 A=0.097
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.981 A=0.019
SGDP_PRJ Global Study-wide 80 G=0.42 A=0.57
The Danish reference pan genome Danish Study-wide 40 G=0.95 A=0.05
Siberian Global Study-wide 6 G=0.5 A=0.5
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 8 NC_000008.11:g.60694186G>A
GRCh37.p13 chr 8 NC_000008.10:g.61606745G>A
CHD7 RefSeqGene (LRG_176) NG_007009.1:g.20407G>A
Gene: CHD7, chromodomain helicase DNA binding protein 7 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHD7 transcript variant 1 NM_017780.4:c.-175+15104G…

NM_017780.4:c.-175+15104G>A

N/A Intron Variant
CHD7 transcript variant 2 NM_001316690.1:c. N/A Genic Upstream Transcript Variant
CHD7 transcript variant X1 XM_011517553.3:c.-175+151…

XM_011517553.3:c.-175+15104G>A

N/A Intron Variant
CHD7 transcript variant X2 XM_011517554.4:c.-175+143…

XM_011517554.4:c.-175+14395G>A

N/A Intron Variant
CHD7 transcript variant X4 XM_011517555.3:c.-175+151…

XM_011517555.3:c.-175+15104G>A

N/A Intron Variant
CHD7 transcript variant X9 XM_011517560.3:c.-175+151…

XM_011517560.3:c.-175+15104G>A

N/A Intron Variant
CHD7 transcript variant X3 XM_017013612.2:c.-175+139…

XM_017013612.2:c.-175+13948G>A

N/A Intron Variant
CHD7 transcript variant X5 XM_017013613.2:c.-175+151…

XM_017013613.2:c.-175+15104G>A

N/A Intron Variant
CHD7 transcript variant X6 XM_047421945.1:c.-175+151…

XM_047421945.1:c.-175+15104G>A

N/A Intron Variant
CHD7 transcript variant X7 XM_047421946.1:c.-175+151…

XM_047421946.1:c.-175+15104G>A

N/A Intron Variant
CHD7 transcript variant X8 XM_047421947.1:c.-175+151…

XM_047421947.1:c.-175+15104G>A

N/A Intron 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 8 NC_000008.11:g.60694186= NC_000008.11:g.60694186G>A
GRCh37.p13 chr 8 NC_000008.10:g.61606745= NC_000008.10:g.61606745G>A
CHD7 RefSeqGene (LRG_176) NG_007009.1:g.20407= NG_007009.1:g.20407G>A
CHD7 transcript variant 1 NM_017780.3:c.-175+15104= NM_017780.3:c.-175+15104G>A
CHD7 transcript variant 1 NM_017780.4:c.-175+15104= NM_017780.4:c.-175+15104G>A
CHD7 transcript variant X1 XM_005251266.1:c.-175+14395= XM_005251266.1:c.-175+14395G>A
CHD7 transcript variant X2 XM_005251267.1:c.-175+15104= XM_005251267.1:c.-175+15104G>A
CHD7 transcript variant X1 XM_011517553.3:c.-175+15104= XM_011517553.3:c.-175+15104G>A
CHD7 transcript variant X2 XM_011517554.4:c.-175+14395= XM_011517554.4:c.-175+14395G>A
CHD7 transcript variant X4 XM_011517555.3:c.-175+15104= XM_011517555.3:c.-175+15104G>A
CHD7 transcript variant X9 XM_011517560.3:c.-175+15104= XM_011517560.3:c.-175+15104G>A
CHD7 transcript variant X3 XM_017013612.2:c.-175+13948= XM_017013612.2:c.-175+13948G>A
CHD7 transcript variant X5 XM_017013613.2:c.-175+15104= XM_017013613.2:c.-175+15104G>A
CHD7 transcript variant X6 XM_047421945.1:c.-175+15104= XM_047421945.1:c.-175+15104G>A
CHD7 transcript variant X7 XM_047421946.1:c.-175+15104= XM_047421946.1:c.-175+15104G>A
CHD7 transcript variant X8 XM_047421947.1:c.-175+15104= XM_047421947.1:c.-175+15104G>A
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#.

60 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23513177 Sep 20, 2004 (123)
2 ABI ss44876246 Mar 15, 2006 (126)
3 AFFY ss66036978 Nov 29, 2006 (127)
4 KRIBB_YJKIM ss83106219 Dec 15, 2007 (130)
5 BCMHGSC_JDW ss93895746 Mar 25, 2008 (129)
6 HUMANGENOME_JCVI ss98077318 Feb 05, 2009 (130)
7 1000GENOMES ss113098642 Jan 25, 2009 (130)
8 ILLUMINA-UK ss115970832 Feb 14, 2009 (130)
9 ENSEMBL ss133505566 Dec 01, 2009 (131)
10 ENSEMBL ss143506932 Dec 01, 2009 (131)
11 ILLUMINA ss160397857 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss164790845 Jul 04, 2010 (132)
13 BUSHMAN ss199227528 Jul 04, 2010 (132)
14 1000GENOMES ss223733899 Jul 14, 2010 (132)
15 1000GENOMES ss234457608 Jul 15, 2010 (132)
16 BL ss254366672 May 09, 2011 (134)
17 PJP ss294091469 May 09, 2011 (134)
18 ILLUMINA ss480808440 Sep 08, 2015 (146)
19 TISHKOFF ss560782947 Apr 25, 2013 (138)
20 SSMP ss655218721 Apr 25, 2013 (138)
21 EVA-GONL ss985573392 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1075561627 Aug 21, 2014 (142)
23 1000GENOMES ss1330077781 Aug 21, 2014 (142)
24 DDI ss1431530356 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1582704906 Apr 01, 2015 (144)
26 EVA_DECODE ss1595169598 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1620755373 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1663749406 Apr 01, 2015 (144)
29 HAMMER_LAB ss1805558077 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1928860359 Feb 12, 2016 (147)
31 JJLAB ss2025132072 Sep 14, 2016 (149)
32 USC_VALOUEV ss2153357430 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2303559455 Dec 20, 2016 (150)
34 GNOMAD ss2867411198 Nov 08, 2017 (151)
35 SWEGEN ss3003270073 Nov 08, 2017 (151)
36 ILLUMINA ss3636911665 Oct 12, 2018 (152)
37 URBANLAB ss3648925925 Oct 12, 2018 (152)
38 EGCUT_WGS ss3670952987 Jul 13, 2019 (153)
39 EVA_DECODE ss3722123536 Jul 13, 2019 (153)
40 ACPOP ss3735710231 Jul 13, 2019 (153)
41 EVA ss3768068320 Jul 13, 2019 (153)
42 KHV_HUMAN_GENOMES ss3811225566 Jul 13, 2019 (153)
43 EVA ss3831191091 Apr 26, 2020 (154)
44 SGDP_PRJ ss3870040433 Apr 26, 2020 (154)
45 KRGDB ss3917557286 Apr 26, 2020 (154)
46 KOGIC ss3963978786 Apr 26, 2020 (154)
47 TOPMED ss4788077215 Apr 26, 2021 (155)
48 TOMMO_GENOMICS ss5188956551 Apr 26, 2021 (155)
49 1000G_HIGH_COVERAGE ss5277335168 Oct 17, 2022 (156)
50 EVA ss5381509012 Oct 17, 2022 (156)
51 HUGCELL_USP ss5473882315 Oct 17, 2022 (156)
52 EVA ss5509376059 Oct 17, 2022 (156)
53 1000G_HIGH_COVERAGE ss5567806992 Oct 17, 2022 (156)
54 SANFORD_IMAGENETICS ss5645491352 Oct 17, 2022 (156)
55 TOMMO_GENOMICS ss5731093554 Oct 17, 2022 (156)
56 YY_MCH ss5809757915 Oct 17, 2022 (156)
57 EVA ss5830609032 Oct 17, 2022 (156)
58 EVA ss5856396394 Oct 17, 2022 (156)
59 EVA ss5889187083 Oct 17, 2022 (156)
60 EVA ss5974702654 Oct 17, 2022 (156)
61 1000Genomes NC_000008.10 - 61606745 Oct 12, 2018 (152)
62 1000Genomes_30x NC_000008.11 - 60694186 Oct 17, 2022 (156)
63 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 61606745 Oct 12, 2018 (152)
64 Genetic variation in the Estonian population NC_000008.10 - 61606745 Oct 12, 2018 (152)
65 The Danish reference pan genome NC_000008.10 - 61606745 Apr 26, 2020 (154)
66 gnomAD - Genomes NC_000008.11 - 60694186 Apr 26, 2021 (155)
67 Genome of the Netherlands Release 5 NC_000008.10 - 61606745 Apr 26, 2020 (154)
68 HapMap NC_000008.11 - 60694186 Apr 26, 2020 (154)
69 KOREAN population from KRGDB NC_000008.10 - 61606745 Apr 26, 2020 (154)
70 Korean Genome Project NC_000008.11 - 60694186 Apr 26, 2020 (154)
71 Northern Sweden NC_000008.10 - 61606745 Jul 13, 2019 (153)
72 Qatari NC_000008.10 - 61606745 Apr 26, 2020 (154)
73 SGDP_PRJ NC_000008.10 - 61606745 Apr 26, 2020 (154)
74 Siberian NC_000008.10 - 61606745 Apr 26, 2020 (154)
75 8.3KJPN NC_000008.10 - 61606745 Apr 26, 2021 (155)
76 14KJPN NC_000008.11 - 60694186 Oct 17, 2022 (156)
77 TopMed NC_000008.11 - 60694186 Apr 26, 2021 (155)
78 UK 10K study - Twins NC_000008.10 - 61606745 Oct 12, 2018 (152)
79 A Vietnamese Genetic Variation Database NC_000008.10 - 61606745 Jul 13, 2019 (153)
80 ALFA NC_000008.11 - 60694186 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).

Associated ID History Updated (Build)
rs59370282 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss93895746, ss113098642, ss115970832, ss164790845, ss199227528, ss254366672, ss294091469, ss1595169598 NC_000008.9:61769298:G:A NC_000008.11:60694185:G:A (self)
42209520, 23474725, 16691235, 8869844, 10480281, 24734680, 8995096, 10902289, 22057413, 5873784, 46925858, 23474725, 5223599, ss223733899, ss234457608, ss480808440, ss560782947, ss655218721, ss985573392, ss1075561627, ss1330077781, ss1431530356, ss1582704906, ss1620755373, ss1663749406, ss1805558077, ss1928860359, ss2025132072, ss2153357430, ss2867411198, ss3003270073, ss3636911665, ss3670952987, ss3735710231, ss3768068320, ss3831191091, ss3870040433, ss3917557286, ss5188956551, ss5381509012, ss5509376059, ss5645491352, ss5830609032, ss5974702654 NC_000008.10:61606744:G:A NC_000008.11:60694185:G:A (self)
55332927, 297637281, 3633355, 20356787, 64930658, 625454775, 2235157326, ss2303559455, ss3648925925, ss3722123536, ss3811225566, ss3963978786, ss4788077215, ss5277335168, ss5473882315, ss5567806992, ss5731093554, ss5809757915, ss5856396394, ss5889187083 NC_000008.11:60694185:G:A NC_000008.11:60694185:G:A (self)
ss23513177, ss44876246, ss66036978, ss83106219, ss98077318, ss133505566, ss143506932, ss160397857 NT_008183.19:13471145:G:A NC_000008.11:60694185: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 rs16926398

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