Name: rs74944644
Published: September 21, 2022
License: Open Access

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.

rs74944644

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:45862654 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.148785 (39382/264690, TOPMED)
C=0.144999 (20310/140070, GnomAD)
C=0.00046 (13/28258, 14KJPN) (+ 15 more)
C=0.16548 (3126/18890, ALFA)
C=0.00036 (6/16760, 8.3KJPN)
C=0.0856 (548/6404, 1000G_30x)
C=0.0859 (430/5008, 1000G)
C=0.1147 (514/4480, Estonian)
C=0.2379 (917/3854, ALSPAC)
C=0.2298 (852/3708, TWINSUK)
C=0.0003 (1/2922, KOREAN)
C=0.114 (114/998, GoNL)
C=0.118 (71/600, NorthernSweden)
C=0.185 (40/216, Qatari)
T=0.46 (37/80, SGDP_PRJ)
C=0.15 (6/40, GENOME_DK)
T=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MAPT-AS1 : 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	18890	T=0.83452	C=0.16548
European	Sub	14286	T=0.80645	C=0.19355
African	Sub	2946	T=0.9549	C=0.0451
African Others	Sub	114	T=0.991	C=0.009
African American	Sub	2832	T=0.9534	C=0.0466
Asian	Sub	112	T=1.000	C=0.000
East Asian	Sub	86	T=1.00	C=0.00
Other Asian	Sub	26	T=1.00	C=0.00
Latin American 1	Sub	146	T=0.801	C=0.199
Latin American 2	Sub	610	T=0.862	C=0.138
South Asian	Sub	98	T=0.92	C=0.08
Other	Sub	692	T=0.845	C=0.155

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.851215	C=0.148785
gnomAD - Genomes	Global	Study-wide	140070	T=0.855001	C=0.144999
gnomAD - Genomes	European	Sub	75838	T=0.80464	C=0.19536
gnomAD - Genomes	African	Sub	41978	T=0.95426	C=0.04574
gnomAD - Genomes	American	Sub	13654	T=0.82357	C=0.17643
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.7604	C=0.2396
gnomAD - Genomes	East Asian	Sub	3132	T=0.9990	C=0.0010
gnomAD - Genomes	Other	Sub	2150	T=0.8293	C=0.1707
14KJPN	JAPANESE	Study-wide	28258	T=0.99954	C=0.00046
Allele Frequency Aggregator	Total	Global	18890	T=0.83452	C=0.16548
Allele Frequency Aggregator	European	Sub	14286	T=0.80645	C=0.19355
Allele Frequency Aggregator	African	Sub	2946	T=0.9549	C=0.0451
Allele Frequency Aggregator	Other	Sub	692	T=0.845	C=0.155
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.862	C=0.138
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.801	C=0.199
Allele Frequency Aggregator	Asian	Sub	112	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.92	C=0.08
8.3KJPN	JAPANESE	Study-wide	16760	T=0.99964	C=0.00036
1000Genomes_30x	Global	Study-wide	6404	T=0.9144	C=0.0856
1000Genomes_30x	African	Sub	1786	T=0.9843	C=0.0157
1000Genomes_30x	Europe	Sub	1266	T=0.7638	C=0.2362
1000Genomes_30x	South Asian	Sub	1202	T=0.9376	C=0.0624
1000Genomes_30x	East Asian	Sub	1170	T=0.9991	C=0.0009
1000Genomes_30x	American	Sub	980	T=0.852	C=0.148
1000Genomes	Global	Study-wide	5008	T=0.9141	C=0.0859
1000Genomes	African	Sub	1322	T=0.9849	C=0.0151
1000Genomes	East Asian	Sub	1008	T=0.9990	C=0.0010
1000Genomes	Europe	Sub	1006	T=0.7604	C=0.2396
1000Genomes	South Asian	Sub	978	T=0.939	C=0.061
1000Genomes	American	Sub	694	T=0.844	C=0.156
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8853	C=0.1147
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.7621	C=0.2379
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.7702	C=0.2298
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9997	C=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.886	C=0.114
Northern Sweden	ACPOP	Study-wide	600	T=0.882	C=0.118
Qatari	Global	Study-wide	216	T=0.815	C=0.185
SGDP_PRJ	Global	Study-wide	80	T=0.46	C=0.54
The Danish reference pan genome	Danish	Study-wide	40	T=0.85	C=0.15
Siberian	Global	Study-wide	4	T=0.5	C=0.5

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 17	NC_000017.11:g.45862654T>C
GRCh37.p13 chr 17	NC_000017.10:g.43940020T>C
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.2:g.925552G>A
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.1:g.927545G>A
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5	NT_187663.1:g.564780T>C

Gene: MAPT-AS1, MAPT antisense RNA 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MAPT-AS1 transcript	NR_024559.1:n.	N/A	Intron Variant

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

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=	C
GRCh38.p14 chr 17	NC_000017.11:g.45862654=	NC_000017.11:g.45862654T>C
GRCh37.p13 chr 17	NC_000017.10:g.43940020=	NC_000017.10:g.43940020T>C
GRCh38.p14 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.2:g.925552G>A	NT_167251.2:g.925552=
GRCh37.p13 chr 17 alt locus HSCHR17_1_CTG5	NT_167251.1:g.927545G>A	NT_167251.1:g.927545=
GRCh38.p14 chr 17 alt locus HSCHR17_2_CTG5	NT_187663.1:g.564780=	NT_187663.1:g.564780T>C

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#.

37 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ENSEMBL	ss137083957	Dec 01, 2009 (131)
2	1000GENOMES	ss237250583	Jul 15, 2010 (137)
3	EVA-GONL	ss993129846	Aug 21, 2014 (142)
4	JMKIDD_LAB	ss1081072765	Aug 21, 2014 (142)
5	1000GENOMES	ss1358745186	Aug 21, 2014 (142)
6	EVA_GENOME_DK	ss1578165580	Apr 01, 2015 (144)
7	EVA_UK10K_ALSPAC	ss1635695532	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1678689565	Apr 01, 2015 (144)
9	EVA_DECODE	ss1697173139	Apr 01, 2015 (144)
10	WEILL_CORNELL_DGM	ss1936591100	Feb 12, 2016 (147)
11	JJLAB	ss2029071713	Sep 14, 2016 (149)
12	USC_VALOUEV	ss2157544672	Dec 20, 2016 (150)
13	HUMAN_LONGEVITY	ss2217018121	Dec 20, 2016 (150)
14	SWEGEN	ss3015573772	Nov 08, 2017 (151)
15	EGCUT_WGS	ss3682455966	Jul 13, 2019 (153)
16	EVA_DECODE	ss3700512047	Jul 13, 2019 (153)
17	ACPOP	ss3742044645	Jul 13, 2019 (153)
18	EVA	ss3754693556	Jul 13, 2019 (153)
19	PACBIO	ss3788211549	Jul 13, 2019 (153)
20	PACBIO	ss3793167503	Jul 13, 2019 (153)
21	PACBIO	ss3798053361	Jul 13, 2019 (153)
22	KHV_HUMAN_GENOMES	ss3819961830	Jul 13, 2019 (153)
23	EVA	ss3834878774	Apr 27, 2020 (154)
24	EVA	ss3846546598	Apr 27, 2020 (154)
25	SGDP_PRJ	ss3885796877	Apr 27, 2020 (154)
26	KRGDB	ss3935495946	Apr 27, 2020 (154)
27	TOPMED	ss5036782894	Apr 27, 2021 (155)
28	TOMMO_GENOMICS	ss5222529029	Apr 27, 2021 (155)
29	1000G_HIGH_COVERAGE	ss5303215567	Oct 16, 2022 (156)
30	EVA	ss5427741120	Oct 16, 2022 (156)
31	HUGCELL_USP	ss5496259824	Oct 16, 2022 (156)
32	EVA	ss5511772695	Oct 16, 2022 (156)
33	1000G_HIGH_COVERAGE	ss5606974272	Oct 16, 2022 (156)
34	SANFORD_IMAGENETICS	ss5660148316	Oct 16, 2022 (156)
35	TOMMO_GENOMICS	ss5778777388	Oct 16, 2022 (156)
36	EVA	ss5834015347	Oct 16, 2022 (156)
37	EVA	ss5951539612	Oct 16, 2022 (156)
38	1000Genomes	NC_000017.10 - 43940020	Oct 12, 2018 (152)
39	1000Genomes_30x	NC_000017.11 - 45862654	Oct 16, 2022 (156)
40	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 43940020	Oct 12, 2018 (152)
41	Genetic variation in the Estonian population	NC_000017.10 - 43940020	Oct 12, 2018 (152)
42	The Danish reference pan genome	NC_000017.10 - 43940020	Apr 27, 2020 (154)
43	gnomAD - Genomes	NC_000017.11 - 45862654	Apr 27, 2021 (155)
44	Genome of the Netherlands Release 5	NC_000017.10 - 43940020	Apr 27, 2020 (154)
45	KOREAN population from KRGDB	NC_000017.10 - 43940020	Apr 27, 2020 (154)
46	Northern Sweden	NC_000017.10 - 43940020	Jul 13, 2019 (153)
47	Qatari	NC_000017.10 - 43940020	Apr 27, 2020 (154)
48	SGDP_PRJ	NC_000017.10 - 43940020	Apr 27, 2020 (154)
49	Siberian	NC_000017.10 - 43940020	Apr 27, 2020 (154)
50	8.3KJPN	NC_000017.10 - 43940020	Apr 27, 2021 (155)
51	14KJPN	NC_000017.11 - 45862654	Oct 16, 2022 (156)
52	TopMed	NC_000017.11 - 45862654	Apr 27, 2021 (155)
53	UK 10K study - Twins	NC_000017.10 - 43940020	Oct 12, 2018 (152)
54	ALFA	NC_000017.11 - 45862654	Apr 27, 2021 (155)

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)
rs117384419	May 04, 2012 (137)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1697173139	NC_000017.9:41295808:T:C	NC_000017.11:45862653:T:C	(self)
71990303, 39896223, 28194214, 4367608, 17780508, 42673340, 15329510, 18633022, 37813857, 10061026, 80498336, 39896223, ss237250583, ss993129846, ss1081072765, ss1358745186, ss1578165580, ss1635695532, ss1678689565, ss1936591100, ss2029071713, ss2157544672, ss3015573772, ss3682455966, ss3742044645, ss3754693556, ss3788211549, ss3793167503, ss3798053361, ss3834878774, ss3885796877, ss3935495946, ss5222529029, ss5427741120, ss5511772695, ss5660148316, ss5834015347, ss5951539612	NC_000017.10:43940019:T:C	NC_000017.11:45862653:T:C	(self)
94500207, 507933265, 112614492, 252328556, 13358201576, ss2217018121, ss3700512047, ss3819961830, ss3846546598, ss5036782894, ss5303215567, ss5496259824, ss5606974272, ss5778777388	NC_000017.11:45862653:T:C	NC_000017.11:45862653:T:C	(self)
ss137083957	NT_010783.15:9214171:T:C	NC_000017.11:45862653:T:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs74944644

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs74944644