Name: rs141281844
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.

rs141281844

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:71524156 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000060 (16/264690, TOPMED)
T=0.000040 (10/249568, GnomAD_exome)
T=0.000057 (8/140190, GnomAD) (+ 7 more)
T=0.000041 (5/120770, ExAC)
T=0.00011 (5/44420, ALFA)
T=0.00011 (3/28258, 14KJPN)
T=0.00012 (2/16760, 8.3KJPN)
T=0.00008 (1/12114, GO-ESP)
T=0.0005 (3/6404, 1000G_30x)
T=0.0004 (2/5008, 1000G)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BDP1 : Missense 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	60778	C=0.99990	T=0.00010
European	Sub	42736	C=0.99988	T=0.00012
African	Sub	8350	C=1.0000	T=0.0000
African Others	Sub	306	C=1.000	T=0.000
African American	Sub	8044	C=1.0000	T=0.0000
Asian	Sub	168	C=1.000	T=0.000
East Asian	Sub	112	C=1.000	T=0.000
Other Asian	Sub	56	C=1.00	T=0.00
Latin American 1	Sub	500	C=1.000	T=0.000
Latin American 2	Sub	628	C=1.000	T=0.000
South Asian	Sub	98	C=1.00	T=0.00
Other	Sub	8298	C=0.9999	T=0.0001

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	C=0.999940	T=0.000060
gnomAD - Exomes	Global	Study-wide	249568	C=0.999960	T=0.000040
gnomAD - Exomes	European	Sub	134840	C=0.999948	T=0.000052
gnomAD - Exomes	Asian	Sub	48580	C=0.99996	T=0.00004
gnomAD - Exomes	American	Sub	34528	C=1.00000	T=0.00000
gnomAD - Exomes	African	Sub	15486	C=0.99994	T=0.00006
gnomAD - Exomes	Ashkenazi Jewish	Sub	10070	C=1.00000	T=0.00000
gnomAD - Exomes	Other	Sub	6064	C=1.0000	T=0.0000
gnomAD - Genomes	Global	Study-wide	140190	C=0.999943	T=0.000057
gnomAD - Genomes	European	Sub	75926	C=0.99995	T=0.00005
gnomAD - Genomes	African	Sub	42014	C=0.99995	T=0.00005
gnomAD - Genomes	American	Sub	13648	C=1.00000	T=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3128	C=0.9994	T=0.0006
gnomAD - Genomes	Other	Sub	2152	C=1.0000	T=0.0000
ExAC	Global	Study-wide	120770	C=0.999959	T=0.000041
ExAC	Europe	Sub	73354	C=0.99997	T=0.00003
ExAC	Asian	Sub	25138	C=0.99992	T=0.00008
ExAC	American	Sub	11576	C=1.00000	T=0.00000
ExAC	African	Sub	9802	C=0.9999	T=0.0001
ExAC	Other	Sub	900	C=1.000	T=0.000
Allele Frequency Aggregator	Total	Global	44420	C=0.99989	T=0.00011
Allele Frequency Aggregator	European	Sub	32650	C=0.99988	T=0.00012
Allele Frequency Aggregator	Other	Sub	6864	C=0.9999	T=0.0001
Allele Frequency Aggregator	African	Sub	3512	C=1.0000	T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	628	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	500	C=1.000	T=0.000
Allele Frequency Aggregator	Asian	Sub	168	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	T=0.00
14KJPN	JAPANESE	Study-wide	28258	C=0.99989	T=0.00011
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99988	T=0.00012
GO Exome Sequencing Project	Global	Study-wide	12114	C=0.99992	T=0.00008
GO Exome Sequencing Project	European American	Sub	8270	C=0.9999	T=0.0001
GO Exome Sequencing Project	African American	Sub	3844	C=1.0000	T=0.0000
1000Genomes_30x	Global	Study-wide	6404	C=0.9995	T=0.0005
1000Genomes_30x	African	Sub	1786	C=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	C=0.9992	T=0.0008
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	T=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.9983	T=0.0017
1000Genomes_30x	American	Sub	980	C=1.000	T=0.000
1000Genomes	Global	Study-wide	5008	C=0.9996	T=0.0004
1000Genomes	African	Sub	1322	C=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	C=0.9990	T=0.0010
1000Genomes	Europe	Sub	1006	C=0.9990	T=0.0010
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
1000Genomes	American	Sub	694	C=1.000	T=0.000

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 5	NC_000005.10:g.71524156C>T
GRCh37.p13 chr 5	NC_000005.9:g.70819983C>T
BDP1 RefSeqGene	NG_047017.1:g.73774C>T
GRCh38.p14 chr 5 alt locus HSCHR5_2_CTG1_1	NW_003315917.2:g.1522641C>T
GRCh38.p14 chr 5 alt locus HSCHR5_1_CTG1_1	NT_187651.1:g.1054131C>T
GRCh38.p14 chr 5 fix patch HG2405_PATCH	NW_025791777.1:g.2011298C>T

Gene: BDP1, B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BDP1 transcript	NM_018429.3:c.5605C>T	R [CGG] > W [TGG]	Coding Sequence Variant
transcription factor TFIIIB component B'' homolog	NP_060899.2:p.Arg1869Trp	R (Arg) > W (Trp)	Missense Variant
BDP1 transcript variant X1	XM_017009630.2:c.5605C>T	R [CGG] > W [TGG]	Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X1	XP_016865119.1:p.Arg1869T… XP_016865119.1:p.Arg1869Trp	R (Arg) > W (Trp)	Missense Variant
BDP1 transcript variant X2	XM_017009631.2:c.5605C>T	R [CGG] > W [TGG]	Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X1	XP_016865120.1:p.Arg1869T… XP_016865120.1:p.Arg1869Trp	R (Arg) > W (Trp)	Missense Variant
BDP1 transcript variant X3	XM_047417372.1:c.5605C>T	R [CGG] > W [TGG]	Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X1	XP_047273328.1:p.Arg1869T… XP_047273328.1:p.Arg1869Trp	R (Arg) > W (Trp)	Missense Variant
BDP1 transcript variant X4	XM_011543511.4:c.5605C>T	R [CGG] > W [TGG]	Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X2	XP_011541813.1:p.Arg1869T… XP_011541813.1:p.Arg1869Trp	R (Arg) > W (Trp)	Missense Variant
BDP1 transcript variant X5	XM_047417373.1:c.5605C>T	R [CGG] > W [TGG]	Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X3	XP_047273329.1:p.Arg1869T… XP_047273329.1:p.Arg1869Trp	R (Arg) > W (Trp)	Missense Variant
BDP1 transcript variant X6	XM_011543512.3:c.5605C>T	R [CGG] > W [TGG]	Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X4	XP_011541814.1:p.Arg1869T… XP_011541814.1:p.Arg1869Trp	R (Arg) > W (Trp)	Missense Variant
BDP1 transcript variant X7	XM_047417374.1:c.5605C>T	R [CGG] > W [TGG]	Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X5	XP_047273330.1:p.Arg1869T… XP_047273330.1:p.Arg1869Trp	R (Arg) > W (Trp)	Missense Variant
BDP1 transcript variant X8	XM_047417375.1:c.5605C>T	R [CGG] > W [TGG]	Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X6	XP_047273331.1:p.Arg1869T… XP_047273331.1:p.Arg1869Trp	R (Arg) > W (Trp)	Missense 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	C=	T
GRCh38.p14 chr 5	NC_000005.10:g.71524156=	NC_000005.10:g.71524156C>T
GRCh37.p13 chr 5	NC_000005.9:g.70819983=	NC_000005.9:g.70819983C>T
BDP1 RefSeqGene	NG_047017.1:g.73774=	NG_047017.1:g.73774C>T
BDP1 transcript	NM_018429.3:c.5605=	NM_018429.3:c.5605C>T
BDP1 transcript	NM_018429.2:c.5605=	NM_018429.2:c.5605C>T
GRCh38.p14 chr 5 alt locus HSCHR5_2_CTG1_1	NW_003315917.2:g.1522641=	NW_003315917.2:g.1522641C>T
GRCh38.p14 chr 5 alt locus HSCHR5_1_CTG1_1	NT_187651.1:g.1054131=	NT_187651.1:g.1054131C>T
GRCh38.p14 chr 5 fix patch HG2405_PATCH	NW_025791777.1:g.2011298=	NW_025791777.1:g.2011298C>T
BDP1 transcript variant X4	XM_011543511.4:c.5605=	XM_011543511.4:c.5605C>T
BDP1 transcript variant X3	XM_011543511.3:c.5605=	XM_011543511.3:c.5605C>T
BDP1 transcript variant X3	XM_011543511.2:c.5605=	XM_011543511.2:c.5605C>T
BDP1 transcript variant X7	XM_011543511.1:c.5605=	XM_011543511.1:c.5605C>T
BDP1 transcript variant X6	XM_011543512.3:c.5605=	XM_011543512.3:c.5605C>T
BDP1 transcript variant X5	XM_011543512.2:c.5605=	XM_011543512.2:c.5605C>T
BDP1 transcript variant X10	XM_011543512.1:c.5605=	XM_011543512.1:c.5605C>T
BDP1 transcript variant X1	XM_017009630.2:c.5605=	XM_017009630.2:c.5605C>T
BDP1 transcript variant X1	XM_017009630.1:c.5605=	XM_017009630.1:c.5605C>T
BDP1 transcript variant X2	XM_017009631.2:c.5605=	XM_017009631.2:c.5605C>T
BDP1 transcript variant X2	XM_017009631.1:c.5605=	XM_017009631.1:c.5605C>T
BDP1 transcript variant X5	XM_047417373.1:c.5605=	XM_047417373.1:c.5605C>T
BDP1 transcript variant X3	XM_047417372.1:c.5605=	XM_047417372.1:c.5605C>T
BDP1 transcript variant X7	XM_047417374.1:c.5605=	XM_047417374.1:c.5605C>T
BDP1 transcript variant X8	XM_047417375.1:c.5605=	XM_047417375.1:c.5605C>T
BDP1 transcript variant X5	XM_047443312.1:c.5605=	XM_047443312.1:c.5605C>T
BDP1 transcript variant X9	XM_047443307.1:c.5605=	XM_047443307.1:c.5605C>T
BDP1 transcript variant X4	XM_047443311.1:c.5605=	XM_047443311.1:c.5605C>T
BDP1 transcript variant X6	XM_047443313.1:c.5605=	XM_047443313.1:c.5605C>T
BDP1 transcript variant X1	XM_047443308.1:c.5605=	XM_047443308.1:c.5605C>T
BDP1 transcript variant X3	XM_047443310.1:c.5605=	XM_047443310.1:c.5605C>T
BDP1 transcript variant X2	XM_047443309.1:c.5605=	XM_047443309.1:c.5605C>T
BDP1 transcript variant X7	XM_047443314.1:c.5605=	XM_047443314.1:c.5605C>T
BDP1 transcript variant X8	XM_047443315.1:c.5605=	XM_047443315.1:c.5605C>T
transcription factor TFIIIB component B'' homolog	NP_060899.2:p.Arg1869=	NP_060899.2:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X2	XP_011541813.1:p.Arg1869=	XP_011541813.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X4	XP_011541814.1:p.Arg1869=	XP_011541814.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X1	XP_016865119.1:p.Arg1869=	XP_016865119.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X1	XP_016865120.1:p.Arg1869=	XP_016865120.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X3	XP_047273329.1:p.Arg1869=	XP_047273329.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X1	XP_047273328.1:p.Arg1869=	XP_047273328.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X5	XP_047273330.1:p.Arg1869=	XP_047273330.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X6	XP_047273331.1:p.Arg1869=	XP_047273331.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X7	XP_047299263.1:p.Arg1869=	XP_047299263.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X1	XP_047299264.1:p.Arg1869=	XP_047299264.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X1	XP_047299265.1:p.Arg1869=	XP_047299265.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X1	XP_047299266.1:p.Arg1869=	XP_047299266.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X2	XP_047299267.1:p.Arg1869=	XP_047299267.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X3	XP_047299268.1:p.Arg1869=	XP_047299268.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X4	XP_047299269.1:p.Arg1869=	XP_047299269.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X5	XP_047299270.1:p.Arg1869=	XP_047299270.1:p.Arg1869Trp
transcription factor TFIIIB component B'' homolog isoform X6	XP_047299271.1:p.Arg1869=	XP_047299271.1:p.Arg1869Trp

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#.

24 SubSNP, 10 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss332534998	May 09, 2011 (134)
2	1000GENOMES	ss490904719	May 04, 2012 (137)
3	NHLBI-ESP	ss712643149	Apr 25, 2013 (138)
4	1000GENOMES	ss1315505060	Aug 21, 2014 (142)
5	EVA_EXAC	ss1687840159	Apr 01, 2015 (144)
6	GNOMAD	ss2735049458	Nov 08, 2017 (151)
7	GNOMAD	ss2747399712	Nov 08, 2017 (151)
8	GNOMAD	ss2825820281	Nov 08, 2017 (151)
9	EVA_DECODE	ss3714882837	Jul 13, 2019 (153)
10	EVA	ss3763552125	Jul 13, 2019 (153)
11	EVA	ss3824088801	Apr 26, 2020 (154)
12	TOPMED	ss4663557126	Apr 26, 2021 (155)
13	TOMMO_GENOMICS	ss5172225287	Apr 26, 2021 (155)
14	EVA	ss5237372884	Apr 26, 2021 (155)
15	1000G_HIGH_COVERAGE	ss5264336636	Oct 17, 2022 (156)
16	EVA	ss5358229121	Oct 17, 2022 (156)
17	1000G_HIGH_COVERAGE	ss5548178125	Oct 17, 2022 (156)
18	TOMMO_GENOMICS	ss5708759814	Oct 17, 2022 (156)
19	EVA	ss5835066052	Oct 17, 2022 (156)
20	EVA	ss5848052004	Oct 17, 2022 (156)
21	EVA	ss5848628362	Oct 17, 2022 (156)
22	EVA	ss5894592096	Oct 17, 2022 (156)
23	EVA	ss5966439995	Oct 17, 2022 (156)
24	EVA	ss5979742307	Oct 17, 2022 (156)
25	1000Genomes	NC_000005.9 - 70819983	Oct 12, 2018 (152)
26	1000Genomes_30x	NC_000005.10 - 71524156	Oct 17, 2022 (156)
27	ExAC	NC_000005.9 - 70819983	Oct 12, 2018 (152)
28	gnomAD - Genomes	NC_000005.10 - 71524156	Apr 26, 2021 (155)
29	gnomAD - Exomes	NC_000005.9 - 70819983	Jul 13, 2019 (153)
30	GO Exome Sequencing Project	NC_000005.9 - 70819983	Oct 12, 2018 (152)
31	8.3KJPN	NC_000005.9 - 70819983	Apr 26, 2021 (155)
32	14KJPN	NC_000005.10 - 71524156	Oct 17, 2022 (156)
33	TopMed	NC_000005.10 - 71524156	Apr 26, 2021 (155)
34	ALFA	NC_000005.10 - 71524156	Apr 26, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
27119953, 7834044, 4168109, 546941, 30194594, ss332534998, ss490904719, ss712643149, ss1315505060, ss1687840159, ss2735049458, ss2747399712, ss2825820281, ss3763552125, ss3824088801, ss5172225287, ss5237372884, ss5358229121, ss5835066052, ss5848052004, ss5848628362, ss5966439995, ss5979742307	NC_000005.9:70819982:C:T	NC_000005.10:71524155:C:T	(self)
35704060, 191722110, 42596918, 500934683, 13060334430, ss3714882837, ss4663557126, ss5264336636, ss5548178125, ss5708759814, ss5894592096	NC_000005.10:71524155:C:T	NC_000005.10:71524155:C:T	(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 rs141281844

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs141281844