Name: rs1490992757
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.

rs1490992757

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:150364376 (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: G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000004 (1/264690, TOPMED)
T=0.000007 (1/140224, GnomAD)
T=0.00000 (0/14050, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TCOF1 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	HWEP
Total	Global	14050	G=1.00000	T=0.00000	1.0	N/A
European	Sub	9690	G=1.0000	T=0.0000	1.0	N/A
African	Sub	2898	G=1.0000	T=0.0000	1.0	N/A
African Others	Sub	114	G=1.000	T=0.000	1.0	N/A
African American	Sub	2784	G=1.0000	T=0.0000	1.0	N/A
Asian	Sub	112	G=1.000	T=0.000	1.0	N/A
East Asian	Sub	86	G=1.00	T=0.00	1.0	N/A
Other Asian	Sub	26	G=1.00	T=0.00	1.0	N/A
Latin American 1	Sub	146	G=1.000	T=0.000	1.0	N/A
Latin American 2	Sub	610	G=1.000	T=0.000	1.0	N/A
South Asian	Sub	98	G=1.00	T=0.00	1.0	N/A
Other	Sub	496	G=1.000	T=0.000	1.0	N/A

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	G=0.999996	T=0.000004
gnomAD - Genomes	Global	Study-wide	140224	G=0.999993	T=0.000007
gnomAD - Genomes	European	Sub	75930	G=0.99999	T=0.00001
gnomAD - Genomes	African	Sub	42026	G=1.00000	T=0.00000
gnomAD - Genomes	American	Sub	13660	G=1.00000	T=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3134	G=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2152	G=1.0000	T=0.0000
Allele Frequency Aggregator	Total	Global	14050	G=1.00000	T=0.00000
Allele Frequency Aggregator	European	Sub	9690	G=1.0000	T=0.0000
Allele Frequency Aggregator	African	Sub	2898	G=1.0000	T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	G=1.000	T=0.000
Allele Frequency Aggregator	Other	Sub	496	G=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	T=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	T=0.00

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.150364376G>T
GRCh37.p13 chr 5	NC_000005.9:g.149743939G>T
TCOF1 RefSeqGene	NG_011341.1:g.11738G>T

Gene: TCOF1, treacle ribosome biogenesis factor 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TCOF1 transcript variant 2	NM_000356.4:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant 3	NM_001008657.3:c.304+124G… NM_001008657.3:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant 4	NM_001135243.2:c.304+124G… NM_001135243.2:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant 5	NM_001135244.2:c.304+124G… NM_001135244.2:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant 6	NM_001135245.2:c.304+124G… NM_001135245.2:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant 7	NM_001195141.2:c.304+124G… NM_001195141.2:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant 8	NM_001371623.1:c.304+124G… NM_001371623.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X1	XM_005268502.5:c.304+124G… XM_005268502.5:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X2	XM_005268503.5:c.304+124G… XM_005268503.5:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X3	XM_005268504.5:c.304+124G… XM_005268504.5:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X5	XM_005268506.5:c.304+124G… XM_005268506.5:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X13	XM_005268507.5:c.304+124G… XM_005268507.5:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X9	XM_011537678.4:c.304+124G… XM_011537678.4:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X7	XM_017009792.3:c.304+124G… XM_017009792.3:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X17	XM_017009793.3:c.304+124G… XM_017009793.3:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X25	XM_017009794.3:c.304+124G… XM_017009794.3:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X42	XM_017009795.3:c.304+124G… XM_017009795.3:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X4	XM_047417645.1:c.304+124G… XM_047417645.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X6	XM_047417646.1:c.304+124G… XM_047417646.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X8	XM_047417647.1:c.304+124G… XM_047417647.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X10	XM_047417648.1:c.304+124G… XM_047417648.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X11	XM_047417649.1:c.304+124G… XM_047417649.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X12	XM_047417650.1:c.304+124G… XM_047417650.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X14	XM_047417651.1:c.304+124G… XM_047417651.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X15	XM_047417652.1:c.304+124G… XM_047417652.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X16	XM_047417653.1:c.304+124G… XM_047417653.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X18	XM_047417654.1:c.304+124G… XM_047417654.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X19	XM_047417655.1:c.304+124G… XM_047417655.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X20	XM_047417656.1:c.304+124G… XM_047417656.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X21	XM_047417657.1:c.304+124G… XM_047417657.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X22	XM_047417658.1:c.304+124G… XM_047417658.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X23	XM_047417659.1:c.304+124G… XM_047417659.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X24	XM_047417660.1:c.304+124G… XM_047417660.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X26	XM_047417661.1:c.304+124G… XM_047417661.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X27	XM_047417662.1:c.304+124G… XM_047417662.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X28	XM_047417663.1:c.304+124G… XM_047417663.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X29	XM_047417664.1:c.304+124G… XM_047417664.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X30	XM_047417665.1:c.304+124G… XM_047417665.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X31	XM_047417666.1:c.304+124G… XM_047417666.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X32	XM_047417667.1:c.304+124G… XM_047417667.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X33	XM_047417668.1:c.304+124G… XM_047417668.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X34	XM_047417669.1:c.304+124G… XM_047417669.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X35	XM_047417670.1:c.304+124G… XM_047417670.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X36	XM_047417671.1:c.304+124G… XM_047417671.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X37	XM_047417672.1:c.304+124G… XM_047417672.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X38	XM_047417673.1:c.304+124G… XM_047417673.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X39	XM_047417674.1:c.304+124G… XM_047417674.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X40	XM_047417675.1:c.304+124G… XM_047417675.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X41	XM_047417676.1:c.304+124G… XM_047417676.1:c.304+124G>T	N/A	Intron Variant
TCOF1 transcript variant X43	XM_047417677.1:c.304+124G… XM_047417677.1:c.304+124G>T	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	G=	T
GRCh38.p14 chr 5	NC_000005.10:g.150364376=	NC_000005.10:g.150364376G>T
GRCh37.p13 chr 5	NC_000005.9:g.149743939=	NC_000005.9:g.149743939G>T
TCOF1 RefSeqGene	NG_011341.1:g.11738=	NG_011341.1:g.11738G>T
TCOF1 transcript variant 2	NM_000356.3:c.304+124=	NM_000356.3:c.304+124G>T
TCOF1 transcript variant 2	NM_000356.4:c.304+124=	NM_000356.4:c.304+124G>T
TCOF1 transcript variant 3	NM_001008657.2:c.304+124=	NM_001008657.2:c.304+124G>T
TCOF1 transcript variant 3	NM_001008657.3:c.304+124=	NM_001008657.3:c.304+124G>T
TCOF1 transcript variant 4	NM_001135243.1:c.304+124=	NM_001135243.1:c.304+124G>T
TCOF1 transcript variant 4	NM_001135243.2:c.304+124=	NM_001135243.2:c.304+124G>T
TCOF1 transcript variant 5	NM_001135244.1:c.304+124=	NM_001135244.1:c.304+124G>T
TCOF1 transcript variant 5	NM_001135244.2:c.304+124=	NM_001135244.2:c.304+124G>T
TCOF1 transcript variant 6	NM_001135245.1:c.304+124=	NM_001135245.1:c.304+124G>T
TCOF1 transcript variant 6	NM_001135245.2:c.304+124=	NM_001135245.2:c.304+124G>T
TCOF1 transcript variant 7	NM_001195141.1:c.304+124=	NM_001195141.1:c.304+124G>T
TCOF1 transcript variant 7	NM_001195141.2:c.304+124=	NM_001195141.2:c.304+124G>T
TCOF1 transcript variant 8	NM_001371623.1:c.304+124=	NM_001371623.1:c.304+124G>T
TCOF1 transcript variant X1	XM_005268502.1:c.304+124=	XM_005268502.1:c.304+124G>T
TCOF1 transcript variant X1	XM_005268502.5:c.304+124=	XM_005268502.5:c.304+124G>T
TCOF1 transcript variant X2	XM_005268503.1:c.304+124=	XM_005268503.1:c.304+124G>T
TCOF1 transcript variant X2	XM_005268503.5:c.304+124=	XM_005268503.5:c.304+124G>T
TCOF1 transcript variant X3	XM_005268504.1:c.304+124=	XM_005268504.1:c.304+124G>T
TCOF1 transcript variant X3	XM_005268504.5:c.304+124=	XM_005268504.5:c.304+124G>T
TCOF1 transcript variant X4	XM_005268505.1:c.304+124=	XM_005268505.1:c.304+124G>T
TCOF1 transcript variant X5	XM_005268506.1:c.304+124=	XM_005268506.1:c.304+124G>T
TCOF1 transcript variant X5	XM_005268506.5:c.304+124=	XM_005268506.5:c.304+124G>T
TCOF1 transcript variant X6	XM_005268507.1:c.304+124=	XM_005268507.1:c.304+124G>T
TCOF1 transcript variant X13	XM_005268507.5:c.304+124=	XM_005268507.5:c.304+124G>T
TCOF1 transcript variant X7	XM_005268508.1:c.304+124=	XM_005268508.1:c.304+124G>T
TCOF1 transcript variant X8	XM_005268509.1:c.304+124=	XM_005268509.1:c.304+124G>T
TCOF1 transcript variant X9	XM_011537678.4:c.304+124=	XM_011537678.4:c.304+124G>T
TCOF1 transcript variant X7	XM_017009792.3:c.304+124=	XM_017009792.3:c.304+124G>T
TCOF1 transcript variant X17	XM_017009793.3:c.304+124=	XM_017009793.3:c.304+124G>T
TCOF1 transcript variant X25	XM_017009794.3:c.304+124=	XM_017009794.3:c.304+124G>T
TCOF1 transcript variant X42	XM_017009795.3:c.304+124=	XM_017009795.3:c.304+124G>T
TCOF1 transcript variant X4	XM_047417645.1:c.304+124=	XM_047417645.1:c.304+124G>T
TCOF1 transcript variant X6	XM_047417646.1:c.304+124=	XM_047417646.1:c.304+124G>T
TCOF1 transcript variant X8	XM_047417647.1:c.304+124=	XM_047417647.1:c.304+124G>T
TCOF1 transcript variant X10	XM_047417648.1:c.304+124=	XM_047417648.1:c.304+124G>T
TCOF1 transcript variant X11	XM_047417649.1:c.304+124=	XM_047417649.1:c.304+124G>T
TCOF1 transcript variant X12	XM_047417650.1:c.304+124=	XM_047417650.1:c.304+124G>T
TCOF1 transcript variant X14	XM_047417651.1:c.304+124=	XM_047417651.1:c.304+124G>T
TCOF1 transcript variant X15	XM_047417652.1:c.304+124=	XM_047417652.1:c.304+124G>T
TCOF1 transcript variant X16	XM_047417653.1:c.304+124=	XM_047417653.1:c.304+124G>T
TCOF1 transcript variant X18	XM_047417654.1:c.304+124=	XM_047417654.1:c.304+124G>T
TCOF1 transcript variant X19	XM_047417655.1:c.304+124=	XM_047417655.1:c.304+124G>T
TCOF1 transcript variant X20	XM_047417656.1:c.304+124=	XM_047417656.1:c.304+124G>T
TCOF1 transcript variant X21	XM_047417657.1:c.304+124=	XM_047417657.1:c.304+124G>T
TCOF1 transcript variant X22	XM_047417658.1:c.304+124=	XM_047417658.1:c.304+124G>T
TCOF1 transcript variant X23	XM_047417659.1:c.304+124=	XM_047417659.1:c.304+124G>T
TCOF1 transcript variant X24	XM_047417660.1:c.304+124=	XM_047417660.1:c.304+124G>T
TCOF1 transcript variant X26	XM_047417661.1:c.304+124=	XM_047417661.1:c.304+124G>T
TCOF1 transcript variant X27	XM_047417662.1:c.304+124=	XM_047417662.1:c.304+124G>T
TCOF1 transcript variant X28	XM_047417663.1:c.304+124=	XM_047417663.1:c.304+124G>T
TCOF1 transcript variant X29	XM_047417664.1:c.304+124=	XM_047417664.1:c.304+124G>T
TCOF1 transcript variant X30	XM_047417665.1:c.304+124=	XM_047417665.1:c.304+124G>T
TCOF1 transcript variant X31	XM_047417666.1:c.304+124=	XM_047417666.1:c.304+124G>T
TCOF1 transcript variant X32	XM_047417667.1:c.304+124=	XM_047417667.1:c.304+124G>T
TCOF1 transcript variant X33	XM_047417668.1:c.304+124=	XM_047417668.1:c.304+124G>T
TCOF1 transcript variant X34	XM_047417669.1:c.304+124=	XM_047417669.1:c.304+124G>T
TCOF1 transcript variant X35	XM_047417670.1:c.304+124=	XM_047417670.1:c.304+124G>T
TCOF1 transcript variant X36	XM_047417671.1:c.304+124=	XM_047417671.1:c.304+124G>T
TCOF1 transcript variant X37	XM_047417672.1:c.304+124=	XM_047417672.1:c.304+124G>T
TCOF1 transcript variant X38	XM_047417673.1:c.304+124=	XM_047417673.1:c.304+124G>T
TCOF1 transcript variant X39	XM_047417674.1:c.304+124=	XM_047417674.1:c.304+124G>T
TCOF1 transcript variant X40	XM_047417675.1:c.304+124=	XM_047417675.1:c.304+124G>T
TCOF1 transcript variant X41	XM_047417676.1:c.304+124=	XM_047417676.1:c.304+124G>T
TCOF1 transcript variant X43	XM_047417677.1:c.304+124=	XM_047417677.1:c.304+124G>T

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#.

2 SubSNP, 3 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss4131649757	Apr 26, 2021 (155)
2	TOPMED	ss4683271212	Apr 26, 2021 (155)
3	gnomAD - Genomes	NC_000005.10 - 150364376	Apr 26, 2021 (155)
4	TopMed	NC_000005.10 - 150364376	Apr 26, 2021 (155)
5	ALFA	NC_000005.10 - 150364376	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
208194608, 520648769, 8344195069, ss4131649757, ss4683271212	NC_000005.10:150364375:G:T	NC_000005.10:150364375:G: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 rs1490992757

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

rs1490992757