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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.

rs547755407

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:33277060-33277068 (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
delGA
Variation Type
Indel Insertion and Deletion
Frequency
(AG)4A=0.411105 (56277/136892, GnomAD)
(AG)4A=0.15709 (4439/28258, 14KJPN)
(AG)4A=0.15412 (2583/16760, 8.3KJPN) (+ 6 more)
(AG)4A=0.44621 (7226/16194, ALFA)
(AG)4A=0.0242 (121/5008, 1000G)
(AG)4A=0.0529 (204/3854, ALSPAC)
(AG)4A=0.0539 (200/3708, TWINSUK)
(AG)4A=0.388 (229/590, NorthernSweden)
(AG)4A=0.45 (18/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
STARD13 : Intron Variant
STARD13-AS : 2KB Upstream 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 16194 AGAGAGAGA=0.44621 AGAGAGA=0.55379 0.178461 0.286032 0.535507 30
European Sub 11942 AGAGAGAGA=0.42129 AGAGAGA=0.57871 0.157093 0.31452 0.528387 22
African Sub 2816 AGAGAGAGA=0.5685 AGAGAGA=0.4315 0.289062 0.151989 0.558949 15
African Others Sub 108 AGAGAGAGA=0.648 AGAGAGA=0.352 0.388889 0.092593 0.518519 1
African American Sub 2708 AGAGAGAGA=0.5654 AGAGAGA=0.4346 0.285081 0.154357 0.560561 15
Asian Sub 108 AGAGAGAGA=0.241 AGAGAGA=0.759 0.018519 0.537037 0.444444 2
East Asian Sub 84 AGAGAGAGA=0.25 AGAGAGA=0.75 0.02381 0.52381 0.452381 1
Other Asian Sub 24 AGAGAGAGA=0.21 AGAGAGA=0.79 0.0 0.583333 0.416667 1
Latin American 1 Sub 146 AGAGAGAGA=0.418 AGAGAGA=0.582 0.150685 0.315068 0.534247 0
Latin American 2 Sub 610 AGAGAGAGA=0.436 AGAGAGA=0.564 0.147541 0.27541 0.577049 6
South Asian Sub 94 AGAGAGAGA=0.33 AGAGAGA=0.67 0.085106 0.425532 0.489362 0
Other Sub 478 AGAGAGAGA=0.439 AGAGAGA=0.561 0.16318 0.284519 0.552301 2


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 136892 (AG)4A=0.411105 delGA=0.588895
gnomAD - Genomes European Sub 74044 (AG)4A=0.36847 delGA=0.63153
gnomAD - Genomes African Sub 41046 (AG)4A=0.53423 delGA=0.46577
gnomAD - Genomes American Sub 13310 (AG)4A=0.34996 delGA=0.65004
gnomAD - Genomes Ashkenazi Jewish Sub 3298 (AG)4A=0.3238 delGA=0.6762
gnomAD - Genomes East Asian Sub 3096 (AG)4A=0.1693 delGA=0.8307
gnomAD - Genomes Other Sub 2098 (AG)4A=0.3889 delGA=0.6111
14KJPN JAPANESE Study-wide 28258 (AG)4A=0.15709 delGA=0.84291
8.3KJPN JAPANESE Study-wide 16760 (AG)4A=0.15412 delGA=0.84588
Allele Frequency Aggregator Total Global 16194 (AG)4A=0.44621 delGA=0.55379
Allele Frequency Aggregator European Sub 11942 (AG)4A=0.42129 delGA=0.57871
Allele Frequency Aggregator African Sub 2816 (AG)4A=0.5685 delGA=0.4315
Allele Frequency Aggregator Latin American 2 Sub 610 (AG)4A=0.436 delGA=0.564
Allele Frequency Aggregator Other Sub 478 (AG)4A=0.439 delGA=0.561
Allele Frequency Aggregator Latin American 1 Sub 146 (AG)4A=0.418 delGA=0.582
Allele Frequency Aggregator Asian Sub 108 (AG)4A=0.241 delGA=0.759
Allele Frequency Aggregator South Asian Sub 94 (AG)4A=0.33 delGA=0.67
1000Genomes Global Study-wide 5008 (AG)4A=0.0242 delGA=0.9758
1000Genomes African Sub 1322 (AG)4A=0.0885 delGA=0.9115
1000Genomes East Asian Sub 1008 (AG)4A=0.0000 delGA=1.0000
1000Genomes Europe Sub 1006 (AG)4A=0.0000 delGA=1.0000
1000Genomes South Asian Sub 978 (AG)4A=0.000 delGA=1.000
1000Genomes American Sub 694 (AG)4A=0.006 delGA=0.994
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (AG)4A=0.0529 delGA=0.9471
UK 10K study - Twins TWIN COHORT Study-wide 3708 (AG)4A=0.0539 delGA=0.9461
Northern Sweden ACPOP Study-wide 590 (AG)4A=0.388 delGA=0.612
The Danish reference pan genome Danish Study-wide 40 (AG)4A=0.45 delGA=0.55
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 13 NC_000013.11:g.33277061GA[3]
GRCh37.p13 chr 13 NC_000013.10:g.33851198GA[3]
STARD13 RefSeqGene NG_029752.2:g.404769CT[3]
Gene: STARD13, StAR related lipid transfer domain containing 13 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
STARD13 transcript variant 4 NM_001243476.3:c.65-10944…

NM_001243476.3:c.65-109445CT[3]

N/A Intron Variant
STARD13 transcript variant 1 NM_178006.4:c.169+8403CT[…

NM_178006.4:c.169+8403CT[3]

N/A Intron Variant
STARD13 transcript variant 5 NM_001243466.2:c. N/A Genic Upstream Transcript Variant
STARD13 transcript variant 6 NM_001243474.2:c. N/A Genic Upstream Transcript Variant
STARD13 transcript variant 3 NM_052851.3:c. N/A Genic Upstream Transcript Variant
STARD13 transcript variant 2 NM_178007.3:c. N/A Genic Upstream Transcript Variant
STARD13 transcript variant X2 XM_017020834.3:c.124+7322…

XM_017020834.3:c.124+73223CT[3]

N/A Intron Variant
STARD13 transcript variant X3 XM_017020835.3:c.65-10944…

XM_017020835.3:c.65-109445CT[3]

N/A Intron Variant
STARD13 transcript variant X2 XM_024449429.2:c.65-10944…

XM_024449429.2:c.65-109445CT[3]

N/A Intron Variant
STARD13 transcript variant X1 XM_047430759.1:c.200-1094…

XM_047430759.1:c.200-109445CT[3]

N/A Intron Variant
STARD13 transcript variant X4 XM_047430760.1:c.65-10944…

XM_047430760.1:c.65-109445CT[3]

N/A Intron Variant
Gene: STARD13-AS, STARD13 antisense RNA (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
STARD13-AS transcript NR_046693.1:n. N/A Upstream 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
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 (AG)4A= delGA
GRCh38.p14 chr 13 NC_000013.11:g.33277060_33277068= NC_000013.11:g.33277061GA[3]
GRCh37.p13 chr 13 NC_000013.10:g.33851197_33851205= NC_000013.10:g.33851198GA[3]
STARD13 RefSeqGene NG_029752.2:g.404768_404776= NG_029752.2:g.404769CT[3]
STARD13 transcript variant 4 NM_001243476.1:c.65-109438= NM_001243476.1:c.65-109445CT[3]
STARD13 transcript variant 4 NM_001243476.3:c.65-109438= NM_001243476.3:c.65-109445CT[3]
STARD13 transcript variant 1 NM_178006.3:c.169+8410= NM_178006.3:c.169+8403CT[3]
STARD13 transcript variant 1 NM_178006.4:c.169+8410= NM_178006.4:c.169+8403CT[3]
STARD13 transcript variant X1 XM_005266586.1:c.124+73230= XM_005266586.1:c.124+73223CT[3]
STARD13 transcript variant X2 XM_017020834.3:c.124+73230= XM_017020834.3:c.124+73223CT[3]
STARD13 transcript variant X3 XM_017020835.3:c.65-109438= XM_017020835.3:c.65-109445CT[3]
STARD13 transcript variant X2 XM_024449429.2:c.65-109438= XM_024449429.2:c.65-109445CT[3]
STARD13 transcript variant X1 XM_047430759.1:c.200-109438= XM_047430759.1:c.200-109445CT[3]
STARD13 transcript variant X4 XM_047430760.1:c.65-109438= XM_047430760.1:c.65-109445CT[3]
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#.

40 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 HUMANGENOME_JCVI ss95616767 Mar 15, 2016 (147)
2 GMI ss155520488 Oct 12, 2018 (152)
3 GMI ss287902733 Oct 12, 2018 (152)
4 GMI ss289170156 Jan 10, 2018 (151)
5 PJP ss294791132 Aug 21, 2014 (142)
6 1000GENOMES ss499944532 Jan 10, 2018 (151)
7 SSMP ss664171906 Jan 10, 2018 (151)
8 1000GENOMES ss1373009018 Jan 10, 2018 (151)
9 DDI ss1536754017 Jan 10, 2018 (151)
10 EVA_GENOME_DK ss1574620209 Jan 10, 2018 (151)
11 EVA_UK10K_ALSPAC ss1707738632 Jan 10, 2018 (151)
12 EVA_UK10K_TWINSUK ss1707738925 Jan 10, 2018 (151)
13 PADH-LAB_SPU ss1751330415 Jan 10, 2018 (151)
14 HAMMER_LAB ss1807557992 Jan 10, 2018 (151)
15 JJLAB ss2031176061 Jan 10, 2018 (151)
16 SYSTEMSBIOZJU ss2628275359 Jan 10, 2018 (151)
17 GNOMAD ss2918320880 Jan 10, 2018 (151)
18 SWEGEN ss3010829161 Jan 10, 2018 (151)
19 MCHAISSO ss3063759640 Jan 10, 2018 (151)
20 MCHAISSO ss3064590714 Jan 10, 2018 (151)
21 BIOINF_KMB_FNS_UNIBA ss3645294733 Oct 12, 2018 (152)
22 URBANLAB ss3650005455 Oct 12, 2018 (152)
23 EVA_DECODE ss3695059146 Jul 13, 2019 (153)
24 ACPOP ss3739642619 Jul 13, 2019 (153)
25 PACBIO ss3787424157 Jul 13, 2019 (153)
26 PACBIO ss3792495516 Jul 13, 2019 (153)
27 PACBIO ss3797379272 Jul 13, 2019 (153)
28 KHV_HUMAN_GENOMES ss3816649243 Jul 13, 2019 (153)
29 EVA ss3833485148 Apr 27, 2020 (154)
30 TOMMO_GENOMICS ss5209467011 Apr 26, 2021 (155)
31 1000G_HIGH_COVERAGE ss5293325575 Oct 16, 2022 (156)
32 HUGCELL_USP ss5487729984 Oct 16, 2022 (156)
33 EVA ss5510930528 Oct 16, 2022 (156)
34 SANFORD_IMAGENETICS ss5654533836 Oct 16, 2022 (156)
35 TOMMO_GENOMICS ss5761192219 Oct 16, 2022 (156)
36 YY_MCH ss5814007975 Oct 16, 2022 (156)
37 EVA ss5839313637 Oct 16, 2022 (156)
38 EVA ss5850676167 Oct 16, 2022 (156)
39 EVA ss5924635308 Oct 16, 2022 (156)
40 EVA ss5945944503 Oct 16, 2022 (156)
41 1000Genomes NC_000013.10 - 33851197 Oct 12, 2018 (152)
42 The Avon Longitudinal Study of Parents and Children NC_000013.10 - 33851197 Oct 12, 2018 (152)
43 The Danish reference pan genome NC_000013.10 - 33851197 Apr 27, 2020 (154)
44 gnomAD - Genomes NC_000013.11 - 33277060 Apr 26, 2021 (155)
45 Northern Sweden NC_000013.10 - 33851197 Jul 13, 2019 (153)
46 8.3KJPN NC_000013.10 - 33851197 Apr 26, 2021 (155)
47 14KJPN NC_000013.11 - 33277060 Oct 16, 2022 (156)
48 UK 10K study - Twins NC_000013.10 - 33851197 Oct 12, 2018 (152)
49 ALFA NC_000013.11 - 33277060 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
ss289170156 NC_000013.9:32749196:AG: NC_000013.11:33277059:AGAGAGAGA:AG…

NC_000013.11:33277059:AGAGAGAGA:AGAGAGA

(self)
ss294791132 NC_000013.9:32749203:GA: NC_000013.11:33277059:AGAGAGAGA:AG…

NC_000013.11:33277059:AGAGAGAGA:AGAGAGA

(self)
60608614, 33665576, 397429, 12927484, 67436318, 33665576, ss499944532, ss664171906, ss1373009018, ss1536754017, ss1574620209, ss1707738632, ss1707738925, ss1751330415, ss1807557992, ss2031176061, ss2628275359, ss2918320880, ss3010829161, ss3739642619, ss3787424157, ss3792495516, ss3797379272, ss3833485148, ss5209467011, ss5510930528, ss5654533836, ss5839313637, ss5945944503 NC_000013.10:33851196:AG: NC_000013.11:33277059:AGAGAGAGA:AG…

NC_000013.11:33277059:AGAGAGAGA:AGAGAGA

(self)
427346749, 95029323, ss3063759640, ss3064590714, ss3645294733, ss3650005455, ss3695059146, ss3816649243, ss5293325575, ss5487729984, ss5761192219, ss5814007975, ss5850676167, ss5924635308 NC_000013.11:33277059:AG: NC_000013.11:33277059:AGAGAGAGA:AG…

NC_000013.11:33277059:AGAGAGAGA:AGAGAGA

(self)
2575896552 NC_000013.11:33277059:AGAGAGAGA:AG…

NC_000013.11:33277059:AGAGAGAGA:AGAGAGA

NC_000013.11:33277059:AGAGAGAGA:AG…

NC_000013.11:33277059:AGAGAGAGA:AGAGAGA

(self)
ss155520488, ss287902733 NT_024524.14:14831196:AG: NC_000013.11:33277059:AGAGAGAGA:AG…

NC_000013.11:33277059:AGAGAGAGA:AGAGAGA

(self)
ss95616767 NT_024524.14:14831203:GA: NC_000013.11:33277059:AGAGAGAGA:AG…

NC_000013.11:33277059:AGAGAGAGA:AGAGAGA

(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 rs547755407

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.post820+afb47a3d