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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.

rs146224299

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:30739337 (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=0.000364 (51/140236, GnomAD)
T=0.00038 (17/44774, ALFA)
T=0.00006 (1/16760, 8.3KJPN) (+ 4 more)
T=0.00038 (5/12994, GO-ESP)
T=0.0003 (1/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
T=0.001 (1/998, GoNL)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SRCAP : Missense Variant
TMEM265 : 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 61136 C=0.99953 A=0.00002, T=0.00046
European Sub 42860 C=0.99949 A=0.00000, T=0.00051
African Sub 8396 C=0.9998 A=0.0000, T=0.0002
African Others Sub 306 C=1.000 A=0.000, T=0.000
African American Sub 8090 C=0.9998 A=0.0000, T=0.0002
Asian Sub 168 C=1.000 A=0.000, T=0.000
East Asian Sub 112 C=1.000 A=0.000, T=0.000
Other Asian Sub 56 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 500 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 628 C=1.000 A=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, T=0.00
Other Sub 8486 C=0.9994 A=0.0001, T=0.0005


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 140236 C=0.999636 T=0.000364
gnomAD - Genomes European Sub 75940 C=0.99951 T=0.00049
gnomAD - Genomes African Sub 42030 C=0.99969 T=0.00031
gnomAD - Genomes American Sub 13658 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=0.9995 T=0.0005
Allele Frequency Aggregator Total Global 44774 C=0.99960 A=0.00002, T=0.00038
Allele Frequency Aggregator European Sub 32770 C=0.99960 A=0.00000, T=0.00040
Allele Frequency Aggregator Other Sub 7052 C=0.9994 A=0.0001, T=0.0004
Allele Frequency Aggregator African Sub 3558 C=0.9997 A=0.0000, T=0.0003
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 168 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
8.3KJPN JAPANESE Study-wide 16760 C=0.99994 T=0.00006
GO Exome Sequencing Project Global Study-wide 12994 C=0.99962 T=0.00038
GO Exome Sequencing Project European American Sub 8600 C=0.9995 T=0.0005
GO Exome Sequencing Project African American Sub 4394 C=0.9998 T=0.0002
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
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.999 T=0.001
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 16 NC_000016.10:g.30739337C>A
GRCh38.p14 chr 16 NC_000016.10:g.30739337C>T
GRCh37.p13 chr 16 NC_000016.9:g.30750658C>A
GRCh37.p13 chr 16 NC_000016.9:g.30750658C>T
SRCAP RefSeqGene NG_032135.1:g.45197C>A
SRCAP RefSeqGene NG_032135.1:g.45197C>T
Gene: TMEM265, transmembrane protein 265 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
TMEM265 transcript NM_001256829.2:c. N/A Upstream Transcript Variant
Gene: SRCAP, Snf2 related CREBBP activator protein (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SRCAP transcript NM_006662.3:c.9297C>A S [AGC] > R [AGA] Coding Sequence Variant
helicase SRCAP NP_006653.2:p.Ser3099Arg S (Ser) > R (Arg) Missense Variant
SRCAP transcript NM_006662.3:c.9297C>T S [AGC] > S [AGT] Coding Sequence Variant
helicase SRCAP NP_006653.2:p.Ser3099= S (Ser) > S (Ser) Synonymous 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.

Allele: T (allele ID: 341224 )
ClinVar Accession Disease Names Clinical Significance
RCV000896855.5 not provided Likely-Benign
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 16 NC_000016.10:g.30739337= NC_000016.10:g.30739337C>A NC_000016.10:g.30739337C>T
GRCh37.p13 chr 16 NC_000016.9:g.30750658= NC_000016.9:g.30750658C>A NC_000016.9:g.30750658C>T
SRCAP RefSeqGene NG_032135.1:g.45197= NG_032135.1:g.45197C>A NG_032135.1:g.45197C>T
SRCAP transcript NM_006662.3:c.9297= NM_006662.3:c.9297C>A NM_006662.3:c.9297C>T
SRCAP transcript NM_006662.2:c.9297= NM_006662.2:c.9297C>A NM_006662.2:c.9297C>T
helicase SRCAP NP_006653.2:p.Ser3099= NP_006653.2:p.Ser3099Arg NP_006653.2:p.Ser3099=
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#.

16 SubSNP, 13 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342426438 May 09, 2011 (134)
2 EVA-GONL ss992430855 Aug 21, 2014 (142)
3 EVA_UK10K_ALSPAC ss1634300848 Apr 01, 2015 (144)
4 EVA_UK10K_TWINSUK ss1677294881 Apr 01, 2015 (144)
5 EVA_EXAC ss1692259624 Apr 01, 2015 (144)
6 EVA_EXAC ss1692259625 Apr 01, 2015 (144)
7 HUMAN_LONGEVITY ss2211718794 Dec 20, 2016 (150)
8 GNOMAD ss2741917405 Nov 08, 2017 (151)
9 GNOMAD ss2749522046 Nov 08, 2017 (151)
10 GNOMAD ss2942090668 Nov 08, 2017 (151)
11 AFFY ss2985065909 Nov 08, 2017 (151)
12 EVA ss3825007871 Apr 27, 2020 (154)
13 TOPMED ss5012777418 Apr 27, 2021 (155)
14 TOPMED ss5012777419 Apr 27, 2021 (155)
15 TOMMO_GENOMICS ss5219185180 Apr 27, 2021 (155)
16 EVA ss5848423382 Oct 17, 2022 (156)
17 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 30750658 Oct 12, 2018 (152)
18 ExAC

Submission ignored due to conflicting rows:
Row 2664099 (NC_000016.9:30750657:C:C 121224/121256, NC_000016.9:30750657:C:T 32/121256)
Row 2664100 (NC_000016.9:30750657:C:C 121251/121256, NC_000016.9:30750657:C:A 5/121256)

- Oct 12, 2018 (152)
19 ExAC

Submission ignored due to conflicting rows:
Row 2664099 (NC_000016.9:30750657:C:C 121224/121256, NC_000016.9:30750657:C:T 32/121256)
Row 2664100 (NC_000016.9:30750657:C:C 121251/121256, NC_000016.9:30750657:C:A 5/121256)

- Oct 12, 2018 (152)
20 gnomAD - Genomes NC_000016.10 - 30739337 Apr 27, 2021 (155)
21 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 11196047 (NC_000016.9:30750657:C:C 251117/251124, NC_000016.9:30750657:C:A 7/251124)
Row 11196048 (NC_000016.9:30750657:C:C 251066/251124, NC_000016.9:30750657:C:T 58/251124)

- Jul 13, 2019 (153)
22 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 11196047 (NC_000016.9:30750657:C:C 251117/251124, NC_000016.9:30750657:C:A 7/251124)
Row 11196048 (NC_000016.9:30750657:C:C 251066/251124, NC_000016.9:30750657:C:T 58/251124)

- Jul 13, 2019 (153)
23 GO Exome Sequencing Project NC_000016.9 - 30750658 Oct 12, 2018 (152)
24 Genome of the Netherlands Release 5 NC_000016.9 - 30750658 Apr 27, 2020 (154)
25 8.3KJPN NC_000016.9 - 30750658 Apr 27, 2021 (155)
26 TopMed

Submission ignored due to conflicting rows:
Row 228323079 (NC_000016.10:30739336:C:A 1/264690)
Row 228323080 (NC_000016.10:30739336:C:T 70/264690)

- Apr 27, 2021 (155)
27 TopMed

Submission ignored due to conflicting rows:
Row 228323079 (NC_000016.10:30739336:C:A 1/264690)
Row 228323080 (NC_000016.10:30739336:C:T 70/264690)

- Apr 27, 2021 (155)
28 UK 10K study - Twins NC_000016.9 - 30750658 Oct 12, 2018 (152)
29 ALFA NC_000016.10 - 30739337 Apr 27, 2021 (155)
30 ClinVar RCV000896855.5 Oct 17, 2022 (156)
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
ss1692259625, ss2741917405 NC_000016.9:30750657:C:A NC_000016.10:30739336:C:A (self)
3024338629, ss5012777418 NC_000016.10:30739336:C:A NC_000016.10:30739336:C:A (self)
38365813, 1465052, 17113401, 77154487, 38365813, ss342426438, ss992430855, ss1634300848, ss1677294881, ss1692259624, ss2741917405, ss2749522046, ss2942090668, ss2985065909, ss3825007871, ss5219185180, ss5848423382 NC_000016.9:30750657:C:T NC_000016.10:30739336:C:T (self)
RCV000896855.5, 487246954, 3024338629, ss2211718794, ss5012777419 NC_000016.10:30739336:C:T NC_000016.10:30739336: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 rs146224299

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