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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.

rs5782265

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:243499641-243499647 (GRCh38.p13) 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
delTTT / dupT
Variation Type
Indel Insertion and Deletion
Frequency
delTTT=0.00000 (0/12858, ALFA)
dupT=0.00000 (0/12858, ALFA)
dupT=0.0615 (308/5008, 1000G) (+ 2 more)
dupT=0.0000 (0/3854, ALSPAC)
dupT=0.0003 (1/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SDCCAG8 : Intron Variant
AKT3 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.243499645_243499647del
GRCh38.p13 chr 1 NC_000001.11:g.243499647dup
GRCh37.p13 chr 1 NC_000001.10:g.243662947_243662949del
GRCh37.p13 chr 1 NC_000001.10:g.243662949dup
AKT3 RefSeqGene (LRG_1396) NG_029764.2:g.356437_356439del
AKT3 RefSeqGene (LRG_1396) NG_029764.2:g.356439dup
GRCh38.p13 chr 1 alt locus HSCHR1_3_CTG32_1 NT_187519.1:g.511753_511755del
GRCh38.p13 chr 1 alt locus HSCHR1_3_CTG32_1 NT_187519.1:g.511755dup
SDCCAG8 RefSeqGene NG_027811.1:g.248641_248643del
SDCCAG8 RefSeqGene NG_027811.1:g.248643dup
Gene: SDCCAG8, SHH signaling and ciliogenesis regulator SDCCAG8 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SDCCAG8 transcript variant 2 NM_001350246.2:c.1210-111…

NM_001350246.2:c.1210-111_1210-109del

N/A Intron Variant
SDCCAG8 transcript variant 3 NM_001350247.2:c.1210-111…

NM_001350247.2:c.1210-111_1210-109del

N/A Intron Variant
SDCCAG8 transcript variant 4 NM_001350248.2:c.2209-111…

NM_001350248.2:c.2209-111_2209-109del

N/A Intron Variant
SDCCAG8 transcript variant 5 NM_001350249.2:c.1819-111…

NM_001350249.2:c.1819-111_1819-109del

N/A Intron Variant
SDCCAG8 transcript variant 6 NM_001350251.2:c.1210-111…

NM_001350251.2:c.1210-111_1210-109del

N/A Intron Variant
SDCCAG8 transcript variant 1 NM_006642.5:c.2113-111_21…

NM_006642.5:c.2113-111_2113-109del

N/A Intron Variant
SDCCAG8 transcript variant X6 XM_005273013.5:c.1984-111…

XM_005273013.5:c.1984-111_1984-109del

N/A Intron Variant
SDCCAG8 transcript variant X13 XM_005273018.2:c.1690-111…

XM_005273018.2:c.1690-111_1690-109del

N/A Intron Variant
SDCCAG8 transcript variant X16 XM_005273022.4:c.1192-111…

XM_005273022.4:c.1192-111_1192-109del

N/A Intron Variant
SDCCAG8 transcript variant X5 XM_011544026.3:c.2002-111…

XM_011544026.3:c.2002-111_2002-109del

N/A Intron Variant
SDCCAG8 transcript variant X11 XM_011544028.3:c.1777-111…

XM_011544028.3:c.1777-111_1777-109del

N/A Intron Variant
SDCCAG8 transcript variant X17 XM_011544030.3:c.1168-111…

XM_011544030.3:c.1168-111_1168-109del

N/A Intron Variant
SDCCAG8 transcript variant X9 XM_017000105.2:c.1876-111…

XM_017000105.2:c.1876-111_1876-109del

N/A Intron Variant
SDCCAG8 transcript variant X7 XM_024452540.1:c.1915-111…

XM_024452540.1:c.1915-111_1915-109del

N/A Intron Variant
SDCCAG8 transcript variant X14 XM_024452548.1:c.1915-111…

XM_024452548.1:c.1915-111_1915-109del

N/A Intron Variant
SDCCAG8 transcript variant X15 XM_024452549.1:c.1582-111…

XM_024452549.1:c.1582-111_1582-109del

N/A Intron Variant
SDCCAG8 transcript variant X1 XM_024452537.1:c.*1769_*1…

XM_024452537.1:c.*1769_*1775=

N/A 3 Prime UTR Variant
SDCCAG8 transcript variant X18 XM_005273023.5:c. N/A Genic Downstream Transcript Variant
SDCCAG8 transcript variant X8 XM_017000104.2:c. N/A Genic Downstream Transcript Variant
SDCCAG8 transcript variant X4 XM_024452539.1:c. N/A Genic Downstream Transcript Variant
SDCCAG8 transcript variant X12 XM_024452547.1:c. N/A Genic Downstream Transcript Variant
SDCCAG8 transcript variant X2 XR_002958955.1:n. N/A Intron Variant
SDCCAG8 transcript variant X3 XR_002958956.1:n. N/A Genic Downstream Transcript Variant
SDCCAG8 transcript variant X10 XR_002958965.1:n. N/A Genic Downstream Transcript Variant
Gene: AKT3, AKT serine/threonine kinase 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
AKT3 transcript variant 2 NM_181690.2:c.*6+94_*6+96…

NM_181690.2:c.*6+94_*6+96del

N/A Intron Variant
AKT3 transcript variant 3 NM_001206729.2:c. N/A Genic Downstream Transcript Variant
AKT3 transcript variant 4 NM_001370074.1:c. N/A Genic Downstream Transcript Variant
AKT3 transcript variant 1 NM_005465.7:c. N/A Genic Downstream Transcript Variant
AKT3 transcript variant X5 XM_011544014.2:c. N/A Genic Downstream Transcript Variant
AKT3 transcript variant X3 XM_016999985.1:c. N/A Genic Downstream Transcript Variant
AKT3 transcript variant X2 XM_024446000.1:c. N/A Genic Downstream Transcript Variant
AKT3 transcript variant X4 XM_024446892.1:c. N/A Genic Downstream Transcript Variant
AKT3 transcript variant X6 XM_024447938.1:c. N/A Genic Downstream Transcript 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 12858 TTTTTTT=1.00000 TTTT=0.00000, TTTTTTTT=0.00000
European Sub 9676 TTTTTTT=1.0000 TTTT=0.0000, TTTTTTTT=0.0000
African Sub 1814 TTTTTTT=1.0000 TTTT=0.0000, TTTTTTTT=0.0000
African Others Sub 48 TTTTTTT=1.00 TTTT=0.00, TTTTTTTT=0.00
African American Sub 1766 TTTTTTT=1.0000 TTTT=0.0000, TTTTTTTT=0.0000
Asian Sub 112 TTTTTTT=1.000 TTTT=0.000, TTTTTTTT=0.000
East Asian Sub 86 TTTTTTT=1.00 TTTT=0.00, TTTTTTTT=0.00
Other Asian Sub 26 TTTTTTT=1.00 TTTT=0.00, TTTTTTTT=0.00
Latin American 1 Sub 134 TTTTTTT=1.000 TTTT=0.000, TTTTTTTT=0.000
Latin American 2 Sub 602 TTTTTTT=1.000 TTTT=0.000, TTTTTTTT=0.000
South Asian Sub 98 TTTTTTT=1.00 TTTT=0.00, TTTTTTTT=0.00
Other Sub 422 TTTTTTT=1.000 TTTT=0.000, TTTTTTTT=0.000


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
1000Genomes Global Study-wide 5008 -

No frequency provided

dupT=0.0615
1000Genomes African Sub 1322 -

No frequency provided

dupT=0.2247
1000Genomes East Asian Sub 1008 -

No frequency provided

dupT=0.0000
1000Genomes Europe Sub 1006 -

No frequency provided

dupT=0.0000
1000Genomes South Asian Sub 978 -

No frequency provided

dupT=0.000
1000Genomes American Sub 694 -

No frequency provided

dupT=0.016
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 -

No frequency provided

dupT=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

dupT=0.0003
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 (T)7= delTTT dupT
GRCh38.p13 chr 1 NC_000001.11:g.243499641_243499647= NC_000001.11:g.243499645_243499647del NC_000001.11:g.243499647dup
GRCh37.p13 chr 1 NC_000001.10:g.243662943_243662949= NC_000001.10:g.243662947_243662949del NC_000001.10:g.243662949dup
AKT3 RefSeqGene (LRG_1396) NG_029764.2:g.356433_356439= NG_029764.2:g.356437_356439del NG_029764.2:g.356439dup
GRCh38.p13 chr 1 alt locus HSCHR1_3_CTG32_1 NT_187519.1:g.511749_511755= NT_187519.1:g.511753_511755del NT_187519.1:g.511755dup
SDCCAG8 RefSeqGene NG_027811.1:g.248637_248643= NG_027811.1:g.248641_248643del NG_027811.1:g.248643dup
SDCCAG8 transcript variant X1 XM_024452537.1:c.*1769_*1775= XM_024452537.1:c.*1773_*1775del XM_024452537.1:c.*1775dup
SDCCAG8 transcript variant 2 NM_001350246.2:c.1210-115= NM_001350246.2:c.1210-111_1210-109del NM_001350246.2:c.1210-109dup
SDCCAG8 transcript variant 3 NM_001350247.2:c.1210-115= NM_001350247.2:c.1210-111_1210-109del NM_001350247.2:c.1210-109dup
SDCCAG8 transcript variant 4 NM_001350248.2:c.2209-115= NM_001350248.2:c.2209-111_2209-109del NM_001350248.2:c.2209-109dup
SDCCAG8 transcript variant 5 NM_001350249.2:c.1819-115= NM_001350249.2:c.1819-111_1819-109del NM_001350249.2:c.1819-109dup
SDCCAG8 transcript variant 6 NM_001350251.2:c.1210-115= NM_001350251.2:c.1210-111_1210-109del NM_001350251.2:c.1210-109dup
SDCCAG8 transcript NM_006642.3:c.2113-115= NM_006642.3:c.2113-111_2113-109del NM_006642.3:c.2113-109dup
SDCCAG8 transcript variant 1 NM_006642.5:c.2113-115= NM_006642.5:c.2113-111_2113-109del NM_006642.5:c.2113-109dup
AKT3 transcript variant 2 NM_181690.2:c.*6+96= NM_181690.2:c.*6+94_*6+96del NM_181690.2:c.*6+90dup
SDCCAG8 transcript variant X2 XM_005273012.1:c.1986-115= XM_005273012.1:c.1986-111_1986-109del XM_005273012.1:c.1986-109dup
SDCCAG8 transcript variant X3 XM_005273013.1:c.1984-115= XM_005273013.1:c.1984-111_1984-109del XM_005273013.1:c.1984-109dup
SDCCAG8 transcript variant X6 XM_005273013.5:c.1984-115= XM_005273013.5:c.1984-111_1984-109del XM_005273013.5:c.1984-109dup
SDCCAG8 transcript variant X4 XM_005273014.1:c.1924-115= XM_005273014.1:c.1924-111_1924-109del XM_005273014.1:c.1924-109dup
SDCCAG8 transcript variant X5 XM_005273015.1:c.1876-115= XM_005273015.1:c.1876-111_1876-109del XM_005273015.1:c.1876-109dup
SDCCAG8 transcript variant X6 XM_005273016.1:c.1819-115= XM_005273016.1:c.1819-111_1819-109del XM_005273016.1:c.1819-109dup
SDCCAG8 transcript variant X7 XM_005273017.1:c.1747-115= XM_005273017.1:c.1747-111_1747-109del XM_005273017.1:c.1747-109dup
SDCCAG8 transcript variant X15 XM_005273018.1:c.1690-115= XM_005273018.1:c.1690-111_1690-109del XM_005273018.1:c.1690-109dup
SDCCAG8 transcript variant X13 XM_005273018.2:c.1690-115= XM_005273018.2:c.1690-111_1690-109del XM_005273018.2:c.1690-109dup
SDCCAG8 transcript variant X9 XM_005273019.1:c.1678-115= XM_005273019.1:c.1678-111_1678-109del XM_005273019.1:c.1678-109dup
SDCCAG8 transcript variant X10 XM_005273020.1:c.1549-115= XM_005273020.1:c.1549-111_1549-109del XM_005273020.1:c.1549-109dup
SDCCAG8 transcript variant X11 XM_005273021.1:c.1210-115= XM_005273021.1:c.1210-111_1210-109del XM_005273021.1:c.1210-109dup
SDCCAG8 transcript variant X12 XM_005273022.1:c.1192-115= XM_005273022.1:c.1192-111_1192-109del XM_005273022.1:c.1192-109dup
SDCCAG8 transcript variant X16 XM_005273022.4:c.1192-115= XM_005273022.4:c.1192-111_1192-109del XM_005273022.4:c.1192-109dup
SDCCAG8 transcript variant X5 XM_011544026.3:c.2002-115= XM_011544026.3:c.2002-111_2002-109del XM_011544026.3:c.2002-109dup
SDCCAG8 transcript variant X11 XM_011544028.3:c.1777-115= XM_011544028.3:c.1777-111_1777-109del XM_011544028.3:c.1777-109dup
SDCCAG8 transcript variant X17 XM_011544030.3:c.1168-115= XM_011544030.3:c.1168-111_1168-109del XM_011544030.3:c.1168-109dup
SDCCAG8 transcript variant X9 XM_017000105.2:c.1876-115= XM_017000105.2:c.1876-111_1876-109del XM_017000105.2:c.1876-109dup
SDCCAG8 transcript variant X7 XM_024452540.1:c.1915-115= XM_024452540.1:c.1915-111_1915-109del XM_024452540.1:c.1915-109dup
SDCCAG8 transcript variant X14 XM_024452548.1:c.1915-115= XM_024452548.1:c.1915-111_1915-109del XM_024452548.1:c.1915-109dup
SDCCAG8 transcript variant X15 XM_024452549.1:c.1582-115= XM_024452549.1:c.1582-111_1582-109del XM_024452549.1:c.1582-109dup
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#.

20 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 ABI ss41191603 Mar 14, 2006 (138)
2 BUSHMAN ss193161399 Jul 04, 2010 (138)
3 1000GENOMES ss499180592 May 04, 2012 (138)
4 LUNTER ss551074173 Apr 25, 2013 (138)
5 TISHKOFF ss554913068 Apr 25, 2013 (138)
6 1000GENOMES ss1368068689 Aug 21, 2014 (142)
7 EVA_UK10K_ALSPAC ss1702026312 Apr 01, 2015 (144)
8 EVA_UK10K_TWINSUK ss1702026314 Apr 01, 2015 (144)
9 HAMMER_LAB ss1796026415 Sep 08, 2015 (146)
10 JJLAB ss2030387893 Sep 14, 2016 (149)
11 GNOMAD ss2768347910 Nov 08, 2017 (151)
12 TOPMED ss3108267977 Nov 08, 2017 (151)
13 TOPMED ss3108267978 Nov 08, 2017 (151)
14 EVA_DECODE ss3689011921 Jul 12, 2019 (153)
15 KHV_HUMAN_GENOMES ss3800579996 Jul 12, 2019 (153)
16 EVA ss3826748462 Apr 25, 2020 (154)
17 EVA ss3986166668 Apr 25, 2021 (155)
18 GNOMAD ss4014531126 Apr 25, 2021 (155)
19 TOPMED ss4490111467 Apr 25, 2021 (155)
20 TOPMED ss4490111468 Apr 25, 2021 (155)
21 1000Genomes NC_000001.10 - 243662943 Oct 11, 2018 (152)
22 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 243662943 Oct 11, 2018 (152)
23 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 44994711 (NC_000001.11:243499640::T 8752/140152)
Row 44994712 (NC_000001.11:243499640:TTT: 1/140172)

- Apr 25, 2021 (155)
24 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 44994711 (NC_000001.11:243499640::T 8752/140152)
Row 44994712 (NC_000001.11:243499640:TTT: 1/140172)

- Apr 25, 2021 (155)
25 TopMed

Submission ignored due to conflicting rows:
Row 33770150 (NC_000001.11:243499640::T 7853/125568)
Row 33770151 (NC_000001.11:243499640:TTT: 1/125568)

- Oct 11, 2018 (152)
26 TopMed

Submission ignored due to conflicting rows:
Row 53717802 (NC_000001.11:243499640::T 17535/264690)
Row 53717803 (NC_000001.11:243499640:TTT: 1/264690)

- Apr 25, 2021 (155)
27 TopMed

Submission ignored due to conflicting rows:
Row 53717802 (NC_000001.11:243499640::T 17535/264690)
Row 53717803 (NC_000001.11:243499640:TTT: 1/264690)

- Apr 25, 2021 (155)
28 UK 10K study - Twins NC_000001.10 - 243662943 Oct 11, 2018 (152)
29 ALFA NC_000001.11 - 243499641 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)
rs34825928 May 15, 2013 (138)
rs67566807 May 11, 2012 (137)
rs67566808 Feb 27, 2009 (130)
rs67566809 Feb 27, 2009 (130)
rs67566810 Feb 27, 2009 (130)
rs67566811 Feb 27, 2009 (130)
rs67566812 Feb 27, 2009 (130)
rs67566813 Feb 27, 2009 (130)
rs67566814 Feb 27, 2009 (130)
rs67566815 Feb 27, 2009 (130)
rs67566816 Feb 27, 2009 (130)
rs67566817 Feb 27, 2009 (130)
rs67566818 Feb 27, 2009 (130)
rs67566819 Feb 27, 2009 (130)
rs67566820 Feb 27, 2009 (130)
rs67566821 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3108267978, ss4014531126, ss4490111468 NC_000001.11:243499640:TTT: NC_000001.11:243499640:TTTTTTT:TTTT (self)
6175436466 NC_000001.11:243499640:TTTTTTT:TTTT NC_000001.11:243499640:TTTTTTT:TTTT (self)
ss551074173 NC_000001.9:241729565::T NC_000001.11:243499640:TTTTTTT:TTT…

NC_000001.11:243499640:TTTTTTT:TTTTTTTT

(self)
6292792, 3483971, 3483971, ss499180592, ss1368068689, ss1702026312, ss1702026314, ss1796026415, ss2030387893, ss2768347910, ss3826748462, ss3986166668 NC_000001.10:243662942::T NC_000001.11:243499640:TTTTTTT:TTT…

NC_000001.11:243499640:TTTTTTT:TTTTTTTT

(self)
ss554913068 NC_000001.10:243662949::T NC_000001.11:243499640:TTTTTTT:TTT…

NC_000001.11:243499640:TTTTTTT:TTTTTTTT

(self)
ss3108267977, ss3689011921, ss3800579996, ss4490111467 NC_000001.11:243499640::T NC_000001.11:243499640:TTTTTTT:TTT…

NC_000001.11:243499640:TTTTTTT:TTTTTTTT

(self)
6175436466 NC_000001.11:243499640:TTTTTTT:TTT…

NC_000001.11:243499640:TTTTTTT:TTTTTTTT

NC_000001.11:243499640:TTTTTTT:TTT…

NC_000001.11:243499640:TTTTTTT:TTTTTTTT

(self)
ss41191603, ss193161399 NT_167186.1:37180721::T NC_000001.11:243499640:TTTTTTT:TTT…

NC_000001.11:243499640:TTTTTTT:TTTTTTTT

(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 rs5782265

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.post596+ae089ad