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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.

rs77532723

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:16011553 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000125 (33/264690, TOPMED)
T=0.000114 (16/140228, GnomAD)
T=0.02594 (733/28258, 14KJPN) (+ 9 more)
T=0.02595 (435/16760, 8.3KJPN)
T=0.00007 (1/14416, ALFA)
T=0.0008 (5/6404, 1000G_30x)
T=0.0010 (5/5008, 1000G)
T=0.0003 (1/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
T=0.0195 (57/2922, KOREAN)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PROM1 : 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 14416 C=0.99993 A=0.00000, T=0.00007
European Sub 9824 C=1.0000 A=0.0000, T=0.0000
African Sub 2946 C=1.0000 A=0.0000, T=0.0000
African Others Sub 114 C=1.000 A=0.000, T=0.000
African American Sub 2832 C=1.0000 A=0.0000, T=0.0000
Asian Sub 108 C=1.000 A=0.000, T=0.000
East Asian Sub 82 C=1.00 A=0.00, T=0.00
Other Asian Sub 26 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 146 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 610 C=1.000 A=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, T=0.00
Other Sub 684 C=0.999 A=0.000, T=0.001


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 C=0.999875 T=0.000125
gnomAD - Genomes Global Study-wide 140228 C=0.999886 T=0.000114
gnomAD - Genomes European Sub 75934 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 42038 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13650 C=0.99993 T=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=0.9952 T=0.0048
gnomAD - Genomes Other Sub 2148 C=1.0000 T=0.0000
14KJPN JAPANESE Study-wide 28258 C=0.97406 T=0.02594
8.3KJPN JAPANESE Study-wide 16760 C=0.97405 T=0.02595
Allele Frequency Aggregator Total Global 14416 C=0.99993 A=0.00000, T=0.00007
Allele Frequency Aggregator European Sub 9824 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2946 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 684 C=0.999 A=0.000, T=0.001
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00, T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9992 T=0.0008
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=0.9957 T=0.0043
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9990 T=0.0010
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=0.9950 T=0.0050
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9997 T=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.0000 T=0.0000
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9805 T=0.0195
SGDP_PRJ Global Study-wide 2 C=0.5 T=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 4 NC_000004.12:g.16011553C>A
GRCh38.p14 chr 4 NC_000004.12:g.16011553C>T
GRCh37.p13 chr 4 NC_000004.11:g.16013176C>A
GRCh37.p13 chr 4 NC_000004.11:g.16013176C>T
PROM1 RefSeqGene NG_011696.2:g.77507G>T
PROM1 RefSeqGene NG_011696.2:g.77507G>A
Gene: PROM1, prominin 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PROM1 transcript variant 2 NM_001145847.2:c.1114+172…

NM_001145847.2:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant 3 NM_001145848.2:c.1114+172…

NM_001145848.2:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant 7 NM_001145849.2:c.1141+172…

NM_001145849.2:c.1141+1722G>T

N/A Intron Variant
PROM1 transcript variant 6 NM_001145850.2:c.1141+172…

NM_001145850.2:c.1141+1722G>T

N/A Intron Variant
PROM1 transcript variant 5 NM_001145851.2:c.1114+172…

NM_001145851.2:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant 4 NM_001145852.2:c.1114+172…

NM_001145852.2:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant 8 NM_001371406.1:c.1114+172…

NM_001371406.1:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant 9 NM_001371407.1:c.1114+172…

NM_001371407.1:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant 10 NM_001371408.1:c.1114+172…

NM_001371408.1:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant 1 NM_006017.3:c.1141+1722G>T N/A Intron Variant
PROM1 transcript variant X15 XM_005248195.6:c.1114+172…

XM_005248195.6:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant X18 XM_005248196.6:c.1114+172…

XM_005248196.6:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant X20 XM_006713974.4:c.907+1722…

XM_006713974.4:c.907+1722G>T

N/A Intron Variant
PROM1 transcript variant X1 XM_011513893.3:c.1141+172…

XM_011513893.3:c.1141+1722G>T

N/A Intron Variant
PROM1 transcript variant X3 XM_011513894.4:c.1141+172…

XM_011513894.4:c.1141+1722G>T

N/A Intron Variant
PROM1 transcript variant X4 XM_011513895.3:c.1141+172…

XM_011513895.3:c.1141+1722G>T

N/A Intron Variant
PROM1 transcript variant X2 XM_011513897.4:c.1141+172…

XM_011513897.4:c.1141+1722G>T

N/A Intron Variant
PROM1 transcript variant X10 XM_011513900.3:c.1141+172…

XM_011513900.3:c.1141+1722G>T

N/A Intron Variant
PROM1 transcript variant X13 XM_011513902.3:c.1141+172…

XM_011513902.3:c.1141+1722G>T

N/A Intron Variant
PROM1 transcript variant X19 XM_011513903.3:c.934+1722…

XM_011513903.3:c.934+1722G>T

N/A Intron Variant
PROM1 transcript variant X12 XM_017008800.2:c.1141+172…

XM_017008800.2:c.1141+1722G>T

N/A Intron Variant
PROM1 transcript variant X5 XM_047416370.1:c.1114+172…

XM_047416370.1:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant X6 XM_047416372.1:c.1114+172…

XM_047416372.1:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant X7 XM_047416373.1:c.1114+172…

XM_047416373.1:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant X8 XM_047416374.1:c.1114+172…

XM_047416374.1:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant X9 XM_047416375.1:c.1114+172…

XM_047416375.1:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant X11 XM_047416376.1:c.1141+172…

XM_047416376.1:c.1141+1722G>T

N/A Intron Variant
PROM1 transcript variant X14 XM_047416377.1:c.1141+172…

XM_047416377.1:c.1141+1722G>T

N/A Intron Variant
PROM1 transcript variant X16 XM_047416378.1:c.1114+172…

XM_047416378.1:c.1114+1722G>T

N/A Intron Variant
PROM1 transcript variant X17 XM_047416379.1:c.1114+172…

XM_047416379.1:c.1114+1722G>T

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 C= A T
GRCh38.p14 chr 4 NC_000004.12:g.16011553= NC_000004.12:g.16011553C>A NC_000004.12:g.16011553C>T
GRCh37.p13 chr 4 NC_000004.11:g.16013176= NC_000004.11:g.16013176C>A NC_000004.11:g.16013176C>T
PROM1 RefSeqGene NG_011696.2:g.77507= NG_011696.2:g.77507G>T NG_011696.2:g.77507G>A
PROM1 transcript variant 2 NM_001145847.1:c.1114+1722= NM_001145847.1:c.1114+1722G>T NM_001145847.1:c.1114+1722G>A
PROM1 transcript variant 2 NM_001145847.2:c.1114+1722= NM_001145847.2:c.1114+1722G>T NM_001145847.2:c.1114+1722G>A
PROM1 transcript variant 3 NM_001145848.1:c.1114+1722= NM_001145848.1:c.1114+1722G>T NM_001145848.1:c.1114+1722G>A
PROM1 transcript variant 3 NM_001145848.2:c.1114+1722= NM_001145848.2:c.1114+1722G>T NM_001145848.2:c.1114+1722G>A
PROM1 transcript variant 7 NM_001145849.1:c.1141+1722= NM_001145849.1:c.1141+1722G>T NM_001145849.1:c.1141+1722G>A
PROM1 transcript variant 7 NM_001145849.2:c.1141+1722= NM_001145849.2:c.1141+1722G>T NM_001145849.2:c.1141+1722G>A
PROM1 transcript variant 6 NM_001145850.1:c.1141+1722= NM_001145850.1:c.1141+1722G>T NM_001145850.1:c.1141+1722G>A
PROM1 transcript variant 6 NM_001145850.2:c.1141+1722= NM_001145850.2:c.1141+1722G>T NM_001145850.2:c.1141+1722G>A
PROM1 transcript variant 5 NM_001145851.1:c.1114+1722= NM_001145851.1:c.1114+1722G>T NM_001145851.1:c.1114+1722G>A
PROM1 transcript variant 5 NM_001145851.2:c.1114+1722= NM_001145851.2:c.1114+1722G>T NM_001145851.2:c.1114+1722G>A
PROM1 transcript variant 4 NM_001145852.1:c.1114+1722= NM_001145852.1:c.1114+1722G>T NM_001145852.1:c.1114+1722G>A
PROM1 transcript variant 4 NM_001145852.2:c.1114+1722= NM_001145852.2:c.1114+1722G>T NM_001145852.2:c.1114+1722G>A
PROM1 transcript variant 8 NM_001371406.1:c.1114+1722= NM_001371406.1:c.1114+1722G>T NM_001371406.1:c.1114+1722G>A
PROM1 transcript variant 9 NM_001371407.1:c.1114+1722= NM_001371407.1:c.1114+1722G>T NM_001371407.1:c.1114+1722G>A
PROM1 transcript variant 10 NM_001371408.1:c.1114+1722= NM_001371408.1:c.1114+1722G>T NM_001371408.1:c.1114+1722G>A
PROM1 transcript variant 1 NM_006017.2:c.1141+1722= NM_006017.2:c.1141+1722G>T NM_006017.2:c.1141+1722G>A
PROM1 transcript variant 1 NM_006017.3:c.1141+1722= NM_006017.3:c.1141+1722G>T NM_006017.3:c.1141+1722G>A
PROM1 transcript variant X1 XM_005248194.1:c.1141+1722= XM_005248194.1:c.1141+1722G>T XM_005248194.1:c.1141+1722G>A
PROM1 transcript variant X2 XM_005248195.1:c.1114+1722= XM_005248195.1:c.1114+1722G>T XM_005248195.1:c.1114+1722G>A
PROM1 transcript variant X15 XM_005248195.6:c.1114+1722= XM_005248195.6:c.1114+1722G>T XM_005248195.6:c.1114+1722G>A
PROM1 transcript variant X3 XM_005248196.1:c.1114+1722= XM_005248196.1:c.1114+1722G>T XM_005248196.1:c.1114+1722G>A
PROM1 transcript variant X18 XM_005248196.6:c.1114+1722= XM_005248196.6:c.1114+1722G>T XM_005248196.6:c.1114+1722G>A
PROM1 transcript variant X20 XM_006713974.4:c.907+1722= XM_006713974.4:c.907+1722G>T XM_006713974.4:c.907+1722G>A
PROM1 transcript variant X1 XM_011513893.3:c.1141+1722= XM_011513893.3:c.1141+1722G>T XM_011513893.3:c.1141+1722G>A
PROM1 transcript variant X3 XM_011513894.4:c.1141+1722= XM_011513894.4:c.1141+1722G>T XM_011513894.4:c.1141+1722G>A
PROM1 transcript variant X4 XM_011513895.3:c.1141+1722= XM_011513895.3:c.1141+1722G>T XM_011513895.3:c.1141+1722G>A
PROM1 transcript variant X2 XM_011513897.4:c.1141+1722= XM_011513897.4:c.1141+1722G>T XM_011513897.4:c.1141+1722G>A
PROM1 transcript variant X10 XM_011513900.3:c.1141+1722= XM_011513900.3:c.1141+1722G>T XM_011513900.3:c.1141+1722G>A
PROM1 transcript variant X13 XM_011513902.3:c.1141+1722= XM_011513902.3:c.1141+1722G>T XM_011513902.3:c.1141+1722G>A
PROM1 transcript variant X19 XM_011513903.3:c.934+1722= XM_011513903.3:c.934+1722G>T XM_011513903.3:c.934+1722G>A
PROM1 transcript variant X12 XM_017008800.2:c.1141+1722= XM_017008800.2:c.1141+1722G>T XM_017008800.2:c.1141+1722G>A
PROM1 transcript variant X5 XM_047416370.1:c.1114+1722= XM_047416370.1:c.1114+1722G>T XM_047416370.1:c.1114+1722G>A
PROM1 transcript variant X6 XM_047416372.1:c.1114+1722= XM_047416372.1:c.1114+1722G>T XM_047416372.1:c.1114+1722G>A
PROM1 transcript variant X7 XM_047416373.1:c.1114+1722= XM_047416373.1:c.1114+1722G>T XM_047416373.1:c.1114+1722G>A
PROM1 transcript variant X8 XM_047416374.1:c.1114+1722= XM_047416374.1:c.1114+1722G>T XM_047416374.1:c.1114+1722G>A
PROM1 transcript variant X9 XM_047416375.1:c.1114+1722= XM_047416375.1:c.1114+1722G>T XM_047416375.1:c.1114+1722G>A
PROM1 transcript variant X11 XM_047416376.1:c.1141+1722= XM_047416376.1:c.1141+1722G>T XM_047416376.1:c.1141+1722G>A
PROM1 transcript variant X14 XM_047416377.1:c.1141+1722= XM_047416377.1:c.1141+1722G>T XM_047416377.1:c.1141+1722G>A
PROM1 transcript variant X16 XM_047416378.1:c.1114+1722= XM_047416378.1:c.1114+1722G>T XM_047416378.1:c.1114+1722G>A
PROM1 transcript variant X17 XM_047416379.1:c.1114+1722= XM_047416379.1:c.1114+1722G>T XM_047416379.1:c.1114+1722G>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#.

19 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss239593598 Jul 15, 2010 (132)
2 1000GENOMES ss1308602381 Aug 21, 2014 (142)
3 EVA_UK10K_ALSPAC ss1609497910 Apr 01, 2015 (144)
4 EVA_UK10K_TWINSUK ss1652491943 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2260746550 Dec 20, 2016 (150)
6 GRF ss2705652446 Nov 08, 2017 (151)
7 GNOMAD ss2806110882 Nov 08, 2017 (151)
8 EVA ss3761451183 Jul 13, 2019 (153)
9 SGDP_PRJ ss3858313412 Apr 26, 2020 (154)
10 KRGDB ss3904462704 Apr 26, 2020 (154)
11 TOPMED ss4604278996 Apr 26, 2021 (155)
12 TOMMO_GENOMICS ss5164392541 Apr 26, 2021 (155)
13 1000G_HIGH_COVERAGE ss5258195115 Oct 17, 2022 (156)
14 EVA ss5347178172 Oct 17, 2022 (156)
15 HUGCELL_USP ss5457078014 Oct 17, 2022 (156)
16 1000G_HIGH_COVERAGE ss5538707495 Oct 17, 2022 (156)
17 TOMMO_GENOMICS ss5698095195 Oct 17, 2022 (156)
18 EVA ss5862315856 Oct 17, 2022 (156)
19 EVA ss5962814633 Oct 17, 2022 (156)
20 1000Genomes NC_000004.11 - 16013176 Oct 12, 2018 (152)
21 1000Genomes_30x NC_000004.12 - 16011553 Oct 17, 2022 (156)
22 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 16013176 Oct 12, 2018 (152)
23 gnomAD - Genomes NC_000004.12 - 16011553 Apr 26, 2021 (155)
24 KOREAN population from KRGDB NC_000004.11 - 16013176 Apr 26, 2020 (154)
25 SGDP_PRJ NC_000004.11 - 16013176 Apr 26, 2020 (154)
26 8.3KJPN NC_000004.11 - 16013176 Apr 26, 2021 (155)
27 14KJPN NC_000004.12 - 16011553 Oct 17, 2022 (156)
28 TopMed NC_000004.12 - 16011553 Apr 26, 2021 (155)
29 UK 10K study - Twins NC_000004.11 - 16013176 Oct 12, 2018 (152)
30 ALFA NC_000004.12 - 16011553 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
2374396163 NC_000004.12:16011552:C:A NC_000004.12:16011552:C:A (self)
19955758, 11113169, 11640098, 10330392, 22361848, 11113169, ss239593598, ss1308602381, ss1609497910, ss1652491943, ss2705652446, ss2806110882, ss3761451183, ss3858313412, ss3904462704, ss5164392541, ss5347178172, ss5962814633 NC_000004.11:16013175:C:T NC_000004.12:16011552:C:T (self)
26233430, 141449545, 31932299, 441656552, 2374396163, ss2260746550, ss4604278996, ss5258195115, ss5457078014, ss5538707495, ss5698095195, ss5862315856 NC_000004.12:16011552:C:T NC_000004.12:16011552:C:T (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 rs77532723

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