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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.

rs752427670

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:71470406-71470413 (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
delT / dupT
Variation Type
Indel Insertion and Deletion
Frequency
dupT=0.000007 (1/139842, GnomAD)
delT=0.000050 (6/119130, ExAC)
dupT=0.00001 (1/76100, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BDP1 : Stop Gained
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 76100 TTTTTTTT=0.99999 TTTTTTTTT=0.00001
European Sub 66652 TTTTTTTT=0.99998 TTTTTTTTT=0.00002
African Sub 3094 TTTTTTTT=1.0000 TTTTTTTTT=0.0000
African Others Sub 136 TTTTTTTT=1.000 TTTTTTTTT=0.000
African American Sub 2958 TTTTTTTT=1.0000 TTTTTTTTT=0.0000
Asian Sub 3270 TTTTTTTT=1.0000 TTTTTTTTT=0.0000
East Asian Sub 2646 TTTTTTTT=1.0000 TTTTTTTTT=0.0000
Other Asian Sub 624 TTTTTTTT=1.000 TTTTTTTTT=0.000
Latin American 1 Sub 436 TTTTTTTT=1.000 TTTTTTTTT=0.000
Latin American 2 Sub 928 TTTTTTTT=1.000 TTTTTTTTT=0.000
South Asian Sub 270 TTTTTTTT=1.000 TTTTTTTTT=0.000
Other Sub 1450 TTTTTTTT=1.0000 TTTTTTTTT=0.0000


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 139842 -

No frequency provided

dupT=0.000007
gnomAD - Genomes European Sub 75742 -

No frequency provided

dupT=0.00001
gnomAD - Genomes African Sub 41916 -

No frequency provided

dupT=0.00000
gnomAD - Genomes American Sub 13596 -

No frequency provided

dupT=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3318 -

No frequency provided

dupT=0.0000
gnomAD - Genomes East Asian Sub 3124 -

No frequency provided

dupT=0.0000
gnomAD - Genomes Other Sub 2146 -

No frequency provided

dupT=0.0000
ExAC Global Study-wide 119130 (T)8=0.999950 delT=0.000050
ExAC Europe Sub 72254 (T)8=0.99993 delT=0.00007
ExAC Asian Sub 24806 (T)8=0.99996 delT=0.00004
ExAC American Sub 11452 (T)8=1.00000 delT=0.00000
ExAC African Sub 9722 (T)8=1.0000 delT=0.0000
ExAC Other Sub 896 (T)8=1.000 delT=0.000
Allele Frequency Aggregator Total Global 76100 (T)8=0.99999 dupT=0.00001
Allele Frequency Aggregator European Sub 66652 (T)8=0.99998 dupT=0.00002
Allele Frequency Aggregator Asian Sub 3270 (T)8=1.0000 dupT=0.0000
Allele Frequency Aggregator African Sub 3094 (T)8=1.0000 dupT=0.0000
Allele Frequency Aggregator Other Sub 1450 (T)8=1.0000 dupT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 928 (T)8=1.000 dupT=0.000
Allele Frequency Aggregator Latin American 1 Sub 436 (T)8=1.000 dupT=0.000
Allele Frequency Aggregator South Asian Sub 270 (T)8=1.000 dupT=0.000
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 5 NC_000005.10:g.71470413del
GRCh38.p14 chr 5 NC_000005.10:g.71470413dup
GRCh37.p13 chr 5 NC_000005.9:g.70766240del
GRCh37.p13 chr 5 NC_000005.9:g.70766240dup
BDP1 RefSeqGene NG_047017.1:g.20031del
BDP1 RefSeqGene NG_047017.1:g.20031dup
GRCh38.p14 chr 5 alt locus HSCHR5_2_CTG1_1 NW_003315917.2:g.1468898del
GRCh38.p14 chr 5 alt locus HSCHR5_2_CTG1_1 NW_003315917.2:g.1468898dup
GRCh38.p14 chr 5 alt locus HSCHR5_1_CTG1_1 NT_187651.1:g.1000399del
GRCh38.p14 chr 5 alt locus HSCHR5_1_CTG1_1 NT_187651.1:g.1000399dup
GRCh38.p14 chr 5 fix patch HG2405_PATCH NW_025791777.1:g.1957566del
GRCh38.p14 chr 5 fix patch HG2405_PATCH NW_025791777.1:g.1957566dup
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.938del L [TTA] > * [TA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog NP_060899.2:p.Phe312_Leu3…

NP_060899.2:p.Phe312_Leu313insTer

L (Leu) > * (Ter) Stop Gained
BDP1 transcript NM_018429.3:c.938dup L [TTA] > F [TTTA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog NP_060899.2:p.Leu313fs L (Leu) > F (Phe) Frameshift Variant
BDP1 transcript variant X1 XM_017009630.2:c.938del L [TTA] > * [TA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X1 XP_016865119.1:p.Phe312_L…

XP_016865119.1:p.Phe312_Leu313insTer

L (Leu) > * (Ter) Stop Gained
BDP1 transcript variant X1 XM_017009630.2:c.938dup L [TTA] > F [TTTA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X1 XP_016865119.1:p.Leu313fs L (Leu) > F (Phe) Frameshift Variant
BDP1 transcript variant X2 XM_017009631.2:c.938del L [TTA] > * [TA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X1 XP_016865120.1:p.Phe312_L…

XP_016865120.1:p.Phe312_Leu313insTer

L (Leu) > * (Ter) Stop Gained
BDP1 transcript variant X2 XM_017009631.2:c.938dup L [TTA] > F [TTTA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X1 XP_016865120.1:p.Leu313fs L (Leu) > F (Phe) Frameshift Variant
BDP1 transcript variant X3 XM_047417372.1:c.938del L [TTA] > * [TA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X1 XP_047273328.1:p.Phe312_L…

XP_047273328.1:p.Phe312_Leu313insTer

L (Leu) > * (Ter) Stop Gained
BDP1 transcript variant X3 XM_047417372.1:c.938dup L [TTA] > F [TTTA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X1 XP_047273328.1:p.Leu313fs L (Leu) > F (Phe) Frameshift Variant
BDP1 transcript variant X4 XM_011543511.4:c.938del L [TTA] > * [TA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X2 XP_011541813.1:p.Phe312_L…

XP_011541813.1:p.Phe312_Leu313insTer

L (Leu) > * (Ter) Stop Gained
BDP1 transcript variant X4 XM_011543511.4:c.938dup L [TTA] > F [TTTA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X2 XP_011541813.1:p.Leu313fs L (Leu) > F (Phe) Frameshift Variant
BDP1 transcript variant X5 XM_047417373.1:c.938del L [TTA] > * [TA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X3 XP_047273329.1:p.Phe312_L…

XP_047273329.1:p.Phe312_Leu313insTer

L (Leu) > * (Ter) Stop Gained
BDP1 transcript variant X5 XM_047417373.1:c.938dup L [TTA] > F [TTTA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X3 XP_047273329.1:p.Leu313fs L (Leu) > F (Phe) Frameshift Variant
BDP1 transcript variant X6 XM_011543512.3:c.938del L [TTA] > * [TA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X4 XP_011541814.1:p.Phe312_L…

XP_011541814.1:p.Phe312_Leu313insTer

L (Leu) > * (Ter) Stop Gained
BDP1 transcript variant X6 XM_011543512.3:c.938dup L [TTA] > F [TTTA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X4 XP_011541814.1:p.Leu313fs L (Leu) > F (Phe) Frameshift Variant
BDP1 transcript variant X7 XM_047417374.1:c.938del L [TTA] > * [TA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X5 XP_047273330.1:p.Phe312_L…

XP_047273330.1:p.Phe312_Leu313insTer

L (Leu) > * (Ter) Stop Gained
BDP1 transcript variant X7 XM_047417374.1:c.938dup L [TTA] > F [TTTA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X5 XP_047273330.1:p.Leu313fs L (Leu) > F (Phe) Frameshift Variant
BDP1 transcript variant X8 XM_047417375.1:c.938del L [TTA] > * [TA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X6 XP_047273331.1:p.Phe312_L…

XP_047273331.1:p.Phe312_Leu313insTer

L (Leu) > * (Ter) Stop Gained
BDP1 transcript variant X8 XM_047417375.1:c.938dup L [TTA] > F [TTTA] Coding Sequence Variant
transcription factor TFIIIB component B'' homolog isoform X6 XP_047273331.1:p.Leu313fs L (Leu) > F (Phe) Frameshift 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 (T)8= delT dupT
GRCh38.p14 chr 5 NC_000005.10:g.71470406_71470413= NC_000005.10:g.71470413del NC_000005.10:g.71470413dup
GRCh37.p13 chr 5 NC_000005.9:g.70766233_70766240= NC_000005.9:g.70766240del NC_000005.9:g.70766240dup
BDP1 RefSeqGene NG_047017.1:g.20024_20031= NG_047017.1:g.20031del NG_047017.1:g.20031dup
BDP1 transcript NM_018429.3:c.931_938= NM_018429.3:c.938del NM_018429.3:c.938dup
BDP1 transcript NM_018429.2:c.931_938= NM_018429.2:c.938del NM_018429.2:c.938dup
GRCh38.p14 chr 5 alt locus HSCHR5_2_CTG1_1 NW_003315917.2:g.1468891_1468898= NW_003315917.2:g.1468898del NW_003315917.2:g.1468898dup
GRCh38.p14 chr 5 alt locus HSCHR5_1_CTG1_1 NT_187651.1:g.1000392_1000399= NT_187651.1:g.1000399del NT_187651.1:g.1000399dup
GRCh38.p14 chr 5 fix patch HG2405_PATCH NW_025791777.1:g.1957559_1957566= NW_025791777.1:g.1957566del NW_025791777.1:g.1957566dup
BDP1 transcript variant X4 XM_011543511.4:c.931_938= XM_011543511.4:c.938del XM_011543511.4:c.938dup
BDP1 transcript variant X3 XM_011543511.3:c.931_938= XM_011543511.3:c.938del XM_011543511.3:c.938dup
BDP1 transcript variant X3 XM_011543511.2:c.931_938= XM_011543511.2:c.938del XM_011543511.2:c.938dup
BDP1 transcript variant X7 XM_011543511.1:c.931_938= XM_011543511.1:c.938del XM_011543511.1:c.938dup
BDP1 transcript variant X6 XM_011543512.3:c.931_938= XM_011543512.3:c.938del XM_011543512.3:c.938dup
BDP1 transcript variant X5 XM_011543512.2:c.931_938= XM_011543512.2:c.938del XM_011543512.2:c.938dup
BDP1 transcript variant X10 XM_011543512.1:c.931_938= XM_011543512.1:c.938del XM_011543512.1:c.938dup
BDP1 transcript variant X1 XM_017009630.2:c.931_938= XM_017009630.2:c.938del XM_017009630.2:c.938dup
BDP1 transcript variant X1 XM_017009630.1:c.931_938= XM_017009630.1:c.938del XM_017009630.1:c.938dup
BDP1 transcript variant X2 XM_017009631.2:c.931_938= XM_017009631.2:c.938del XM_017009631.2:c.938dup
BDP1 transcript variant X2 XM_017009631.1:c.931_938= XM_017009631.1:c.938del XM_017009631.1:c.938dup
BDP1 transcript variant X5 XM_047417373.1:c.931_938= XM_047417373.1:c.938del XM_047417373.1:c.938dup
BDP1 transcript variant X3 XM_047417372.1:c.931_938= XM_047417372.1:c.938del XM_047417372.1:c.938dup
BDP1 transcript variant X7 XM_047417374.1:c.931_938= XM_047417374.1:c.938del XM_047417374.1:c.938dup
BDP1 transcript variant X8 XM_047417375.1:c.931_938= XM_047417375.1:c.938del XM_047417375.1:c.938dup
BDP1 transcript variant X5 XM_047443312.1:c.931_938= XM_047443312.1:c.938del XM_047443312.1:c.938dup
BDP1 transcript variant X9 XM_047443307.1:c.931_938= XM_047443307.1:c.938del XM_047443307.1:c.938dup
BDP1 transcript variant X4 XM_047443311.1:c.931_938= XM_047443311.1:c.938del XM_047443311.1:c.938dup
BDP1 transcript variant X6 XM_047443313.1:c.931_938= XM_047443313.1:c.938del XM_047443313.1:c.938dup
BDP1 transcript variant X1 XM_047443308.1:c.931_938= XM_047443308.1:c.938del XM_047443308.1:c.938dup
BDP1 transcript variant X3 XM_047443310.1:c.931_938= XM_047443310.1:c.938del XM_047443310.1:c.938dup
BDP1 transcript variant X2 XM_047443309.1:c.931_938= XM_047443309.1:c.938del XM_047443309.1:c.938dup
BDP1 transcript variant X7 XM_047443314.1:c.931_938= XM_047443314.1:c.938del XM_047443314.1:c.938dup
BDP1 transcript variant X8 XM_047443315.1:c.931_938= XM_047443315.1:c.938del XM_047443315.1:c.938dup
transcription factor TFIIIB component B'' homolog NP_060899.2:p.Phe311_Leu313= NP_060899.2:p.Phe312_Leu313insTer NP_060899.2:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X2 XP_011541813.1:p.Phe311_Leu313= XP_011541813.1:p.Phe312_Leu313insTer XP_011541813.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X4 XP_011541814.1:p.Phe311_Leu313= XP_011541814.1:p.Phe312_Leu313insTer XP_011541814.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X1 XP_016865119.1:p.Phe311_Leu313= XP_016865119.1:p.Phe312_Leu313insTer XP_016865119.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X1 XP_016865120.1:p.Phe311_Leu313= XP_016865120.1:p.Phe312_Leu313insTer XP_016865120.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X3 XP_047273329.1:p.Phe311_Leu313= XP_047273329.1:p.Phe312_Leu313insTer XP_047273329.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X1 XP_047273328.1:p.Phe311_Leu313= XP_047273328.1:p.Phe312_Leu313insTer XP_047273328.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X5 XP_047273330.1:p.Phe311_Leu313= XP_047273330.1:p.Phe312_Leu313insTer XP_047273330.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X6 XP_047273331.1:p.Phe311_Leu313= XP_047273331.1:p.Phe312_Leu313insTer XP_047273331.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X7 XP_047299263.1:p.Phe311_Leu313= XP_047299263.1:p.Phe312_Leu313insTer XP_047299263.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X1 XP_047299264.1:p.Phe311_Leu313= XP_047299264.1:p.Phe312_Leu313insTer XP_047299264.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X1 XP_047299265.1:p.Phe311_Leu313= XP_047299265.1:p.Phe312_Leu313insTer XP_047299265.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X1 XP_047299266.1:p.Phe311_Leu313= XP_047299266.1:p.Phe312_Leu313insTer XP_047299266.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X2 XP_047299267.1:p.Phe311_Leu313= XP_047299267.1:p.Phe312_Leu313insTer XP_047299267.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X3 XP_047299268.1:p.Phe311_Leu313= XP_047299268.1:p.Phe312_Leu313insTer XP_047299268.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X4 XP_047299269.1:p.Phe311_Leu313= XP_047299269.1:p.Phe312_Leu313insTer XP_047299269.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X5 XP_047299270.1:p.Phe311_Leu313= XP_047299270.1:p.Phe312_Leu313insTer XP_047299270.1:p.Leu313fs
transcription factor TFIIIB component B'' homolog isoform X6 XP_047299271.1:p.Phe311_Leu313= XP_047299271.1:p.Phe312_Leu313insTer XP_047299271.1:p.Leu313fs
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#.

3 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1711788357 Apr 01, 2015 (144)
2 GNOMAD ss2747399259 Nov 08, 2017 (151)
3 GNOMAD ss2825815869 Nov 08, 2017 (151)
4 ExAC NC_000005.9 - 70766233 Oct 12, 2018 (152)
5 gnomAD - Genomes NC_000005.10 - 71470406 Apr 26, 2021 (155)
6 ALFA NC_000005.10 - 71470406 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
7832922, ss1711788357 NC_000005.9:70766232:T: NC_000005.10:71470405:TTTTTTTT:TTT…

NC_000005.10:71470405:TTTTTTTT:TTTTTTT

(self)
ss2747399259, ss2825815869 NC_000005.9:70766232::T NC_000005.10:71470405:TTTTTTTT:TTT…

NC_000005.10:71470405:TTTTTTTT:TTTTTTTTT

(self)
191710954 NC_000005.10:71470405::T NC_000005.10:71470405:TTTTTTTT:TTT…

NC_000005.10:71470405:TTTTTTTT:TTTTTTTTT

(self)
1816120798 NC_000005.10:71470405:TTTTTTTT:TTT…

NC_000005.10:71470405:TTTTTTTT:TTTTTTTTT

NC_000005.10:71470405:TTTTTTTT:TTT…

NC_000005.10:71470405:TTTTTTTT:TTTTTTTTT

(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 rs752427670

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.post774+babeb33