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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.

rs72502741

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:281877-281878 (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=0.137576 (17339/126032, GnomAD)
delC=0.25182 (6710/26646, 14KJPN)
delC=0.14475 (2659/18370, ALFA) (+ 6 more)
delC=0.25174 (3981/15814, 8.3KJPN)
delC=0.1460 (935/6404, 1000G_30x)
delC=0.1392 (697/5008, 1000G)
delC=0.3082 (503/1632, Korea1K)
delC=0.209 (121/580, NorthernSweden)
delC=0.21 (8/38, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC124903815 : Non Coding Transcript 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 18370 CC=0.85525 C=0.14475
European Sub 14002 CC=0.83188 C=0.16812
African Sub 2898 CC=0.9462 C=0.0538
African Others Sub 114 CC=0.965 C=0.035
African American Sub 2784 CC=0.9454 C=0.0546
Asian Sub 112 CC=0.759 C=0.241
East Asian Sub 86 CC=0.74 C=0.26
Other Asian Sub 26 CC=0.81 C=0.19
Latin American 1 Sub 146 CC=0.932 C=0.068
Latin American 2 Sub 610 CC=0.907 C=0.093
South Asian Sub 98 CC=0.91 C=0.09
Other Sub 504 CC=0.909 C=0.091


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 126032 CC=0.862424 delC=0.137576
gnomAD - Genomes European Sub 68938 CC=0.81393 delC=0.18607
gnomAD - Genomes African Sub 37592 CC=0.94523 delC=0.05477
gnomAD - Genomes American Sub 11972 CC=0.90085 delC=0.09915
gnomAD - Genomes Ashkenazi Jewish Sub 3108 CC=0.9463 delC=0.0537
gnomAD - Genomes East Asian Sub 2544 CC=0.6588 delC=0.3412
gnomAD - Genomes Other Sub 1878 CC=0.8770 delC=0.1230
14KJPN JAPANESE Study-wide 26646 CC=0.74818 delC=0.25182
Allele Frequency Aggregator Total Global 18370 CC=0.85525 delC=0.14475
Allele Frequency Aggregator European Sub 14002 CC=0.83188 delC=0.16812
Allele Frequency Aggregator African Sub 2898 CC=0.9462 delC=0.0538
Allele Frequency Aggregator Latin American 2 Sub 610 CC=0.907 delC=0.093
Allele Frequency Aggregator Other Sub 504 CC=0.909 delC=0.091
Allele Frequency Aggregator Latin American 1 Sub 146 CC=0.932 delC=0.068
Allele Frequency Aggregator Asian Sub 112 CC=0.759 delC=0.241
Allele Frequency Aggregator South Asian Sub 98 CC=0.91 delC=0.09
8.3KJPN JAPANESE Study-wide 15814 CC=0.74826 delC=0.25174
1000Genomes_30x Global Study-wide 6404 CC=0.8540 delC=0.1460
1000Genomes_30x African Sub 1786 CC=0.9597 delC=0.0403
1000Genomes_30x Europe Sub 1266 CC=0.8025 delC=0.1975
1000Genomes_30x South Asian Sub 1202 CC=0.8577 delC=0.1423
1000Genomes_30x East Asian Sub 1170 CC=0.7068 delC=0.2932
1000Genomes_30x American Sub 980 CC=0.899 delC=0.101
1000Genomes Global Study-wide 5008 CC=0.8608 delC=0.1392
1000Genomes African Sub 1322 CC=0.9554 delC=0.0446
1000Genomes East Asian Sub 1008 CC=0.7262 delC=0.2738
1000Genomes Europe Sub 1006 CC=0.8280 delC=0.1720
1000Genomes South Asian Sub 978 CC=0.875 delC=0.125
1000Genomes American Sub 694 CC=0.903 delC=0.097
Korean Genome Project KOREAN Study-wide 1632 CC=0.6918 delC=0.3082
Northern Sweden ACPOP Study-wide 580 CC=0.791 delC=0.209
The Danish reference pan genome Danish Study-wide 38 CC=0.79 delC=0.21
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 1 NC_000001.11:g.281878del
GRCh37.p13 chr 1 NC_000001.10:g.251629del
Gene: LOC124903815, uncharacterized LOC124903815 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124903815 transcript variant X1 XR_007065335.1:n.851del N/A Non Coding Transcript Variant
LOC124903815 transcript variant X2 XR_007065336.1:n. 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 CC= delC
GRCh38.p14 chr 1 NC_000001.11:g.281877_281878= NC_000001.11:g.281878del
GRCh37.p13 chr 1 NC_000001.10:g.251628_251629= NC_000001.10:g.251629del
LOC124903815 transcript variant X1 XR_007065335.1:n.850_851= XR_007065335.1:n.851del
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#.

28 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 BGI ss104663001 Feb 13, 2009 (130)
2 GMI ss229263623 May 09, 2011 (147)
3 BL ss255892547 May 09, 2011 (137)
4 GMI ss287939224 May 04, 2012 (137)
5 1000GENOMES ss498763777 May 04, 2012 (137)
6 LUNTER ss550903093 Apr 25, 2013 (138)
7 LUNTER ss552738962 Apr 25, 2013 (138)
8 SSMP ss663177885 Apr 01, 2015 (144)
9 1000GENOMES ss1367645247 Aug 21, 2014 (142)
10 EVA_GENOME_DK ss1573867278 Apr 01, 2015 (144)
11 JJLAB ss2030297685 Sep 14, 2016 (149)
12 GNOMAD ss2750616191 Nov 08, 2017 (151)
13 SWEGEN ss2986144424 Nov 08, 2017 (151)
14 MCHAISSO ss3063573446 Nov 08, 2017 (151)
15 MCHAISSO ss3064385962 Nov 08, 2017 (151)
16 MCHAISSO ss3065282437 Nov 08, 2017 (151)
17 EVA_DECODE ss3685991078 Jul 12, 2019 (153)
18 ACPOP ss3726715525 Jul 12, 2019 (153)
19 KHV_HUMAN_GENOMES ss3798742682 Jul 12, 2019 (153)
20 KOGIC ss3943625175 Apr 25, 2020 (154)
21 TOMMO_GENOMICS ss5142040379 Apr 25, 2021 (155)
22 HUGCELL_USP ss5442111275 Oct 12, 2022 (156)
23 1000G_HIGH_COVERAGE ss5512480839 Oct 12, 2022 (156)
24 SANFORD_IMAGENETICS ss5624744986 Oct 12, 2022 (156)
25 TOMMO_GENOMICS ss5666176200 Oct 12, 2022 (156)
26 YY_MCH ss5800241767 Oct 12, 2022 (156)
27 EVA ss5831417080 Oct 12, 2022 (156)
28 EVA ss5936581945 Oct 12, 2022 (156)
29 1000Genomes NC_000001.10 - 251628 Oct 11, 2018 (152)
30 1000Genomes_30x NC_000001.11 - 281877 Oct 12, 2022 (156)
31 The Danish reference pan genome NC_000001.10 - 251628 Apr 25, 2020 (154)
32 gnomAD - Genomes NC_000001.11 - 281877 Apr 25, 2021 (155)
33 Korean Genome Project NC_000001.11 - 281877 Apr 25, 2020 (154)
34 Northern Sweden NC_000001.10 - 251628 Jul 12, 2019 (153)
35 8.3KJPN NC_000001.10 - 251628 Apr 25, 2021 (155)
36 14KJPN NC_000001.11 - 281877 Oct 12, 2022 (156)
37 ALFA NC_000001.11 - 281877 Apr 25, 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)
rs147095472 Jul 19, 2016 (147)
rs149773139 May 04, 2012 (137)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss255892547, ss287939224, ss550903093, ss552738962 NC_000001.9:241490:C: NC_000001.11:281876:CC:C (self)
1167, 120171, 390, 9686, ss498763777, ss663177885, ss1367645247, ss1573867278, ss2030297685, ss2750616191, ss2986144424, ss3726715525, ss5142040379, ss5624744986, ss5831417080, ss5936581945 NC_000001.10:251627:C: NC_000001.11:281876:CC:C (self)
6774, 27975, 3176, 13304, ss3063573446, ss3064385962, ss3065282437, ss3685991078, ss3798742682, ss3943625175, ss5442111275, ss5512480839, ss5666176200, ss5800241767 NC_000001.11:281876:C: NC_000001.11:281876:CC:C (self)
11775294411 NC_000001.11:281876:CC:C NC_000001.11:281876:CC:C (self)
ss104663001 NT_077402.2:241627:CC:C NC_000001.11:281876:CC:C (self)
ss229263623 NT_187170.1:24210:C: NC_000001.11:281876: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 rs72502741

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