Name: rs772166980
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.

rs772166980

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:53459574 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.000008 (2/264690, TOPMED)
G=0.00007 (1/14050, ALFA)
G=0.0000 (0/3854, ALSPAC) (+ 1 more)
G=0.0003 (1/3708, TWINSUK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FIP1L1 : Non Coding Transcript Variant
LNX1 : 3 Prime UTR 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	14050	A=0.99993	G=0.00007
European	Sub	9690	A=1.0000	G=0.0000
African	Sub	2898	A=1.0000	G=0.0000
African Others	Sub	114	A=1.000	G=0.000
African American	Sub	2784	A=1.0000	G=0.0000
Asian	Sub	112	A=1.000	G=0.000
East Asian	Sub	86	A=1.00	G=0.00
Other Asian	Sub	26	A=1.00	G=0.00
Latin American 1	Sub	146	A=1.000	G=0.000
Latin American 2	Sub	610	A=1.000	G=0.000
South Asian	Sub	98	A=1.00	G=0.00
Other	Sub	496	A=0.998	G=0.002

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	A=0.999992	G=0.000008
Allele Frequency Aggregator	Total	Global	14050	A=0.99993	G=0.00007
Allele Frequency Aggregator	European	Sub	9690	A=1.0000	G=0.0000
Allele Frequency Aggregator	African	Sub	2898	A=1.0000	G=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	A=1.000	G=0.000
Allele Frequency Aggregator	Other	Sub	496	A=0.998	G=0.002
Allele Frequency Aggregator	Latin American 1	Sub	146	A=1.000	G=0.000
Allele Frequency Aggregator	Asian	Sub	112	A=1.000	G=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=1.00	G=0.00
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=1.0000	G=0.0000
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9997	G=0.0003

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 4	NC_000004.12:g.53459574A>G
GRCh37.p13 chr 4	NC_000004.11:g.54325741A>G
FIP1L1 RefSeqGene	NG_008644.1:g.86922A>G

Gene: FIP1L1, factor interacting with PAPOLA and CPSF1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FIP1L1 transcript variant 1	NM_030917.4:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 25	NM_001376766.1:c.*46=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 5	NM_001376745.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 44	NM_001376785.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 8	NM_001376748.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 27	NM_001376768.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 13	NM_001376753.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 40	NM_001376781.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 16	NM_001376756.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 28	NM_001376769.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 17	NM_001376757.1:c.*46=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 10	NM_001376750.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 38	NM_001376779.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 14	NM_001376754.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 19	NM_001376759.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 7	NM_001376747.1:c.*46=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 30	NM_001376771.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 23	NM_001376764.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 35	NM_001376776.1:c.*46=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 29	NM_001376770.1:c.*46=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 45	NM_001376786.1:c.*46=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 36	NM_001376777.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 15	NM_001376755.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 12	NM_001376752.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 21	NM_001376761.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 11	NM_001376751.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 41	NM_001376782.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 2	NM_001134937.2:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 9	NM_001376749.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 34	NM_001376775.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 33	NM_001376774.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 20	NM_001376760.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 43	NM_001376784.1:c.*46=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 22	NM_001376762.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 32	NM_001376773.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 3	NM_001134938.2:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 24	NM_001376765.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 4	NM_001376744.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 6	NM_001376746.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 26	NM_001376767.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 39	NM_001376780.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 18	NM_001376758.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 31	NM_001376772.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 37	NM_001376778.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 42	NM_001376783.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant 47	NR_164848.1:n.2227A>G	N/A	Non Coding Transcript Variant
FIP1L1 transcript variant 48	NR_164849.1:n.2020A>G	N/A	Non Coding Transcript Variant
FIP1L1 transcript variant 46	NR_164847.1:n.1927A>G	N/A	Non Coding Transcript Variant
FIP1L1 transcript variant X1	XM_047416208.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant X2	XM_047416209.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant X2	XM_047416210.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant X3	XM_047416211.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant X4	XM_047416212.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant X5	XM_047416213.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant X6	XM_047416214.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant X7	XM_005265779.5:c.*46=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant X8	XM_047416215.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant X9	XM_047416216.1:c.*125=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant X11	XM_047416217.1:c.*46=	N/A	3 Prime UTR Variant
FIP1L1 transcript variant X10	XM_047416218.1:c.*46=	N/A	3 Prime UTR Variant

Gene: LNX1, ligand of numb-protein X 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LNX1 transcript variant 1	NM_001126328.3:c.*1333=	N/A	3 Prime UTR Variant
LNX1 transcript variant 2	NM_032622.3:c.*1333=	N/A	3 Prime UTR Variant
LNX1 transcript variant X1	XM_024454262.2:c.*1333=	N/A	3 Prime UTR Variant
LNX1 transcript variant X2	XM_005265785.6:c.*1333=	N/A	3 Prime UTR Variant
LNX1 transcript variant X3	XM_047416328.1:c.	N/A	Genic Downstream Transcript 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	A=	G
GRCh38.p14 chr 4	NC_000004.12:g.53459574=	NC_000004.12:g.53459574A>G
GRCh37.p13 chr 4	NC_000004.11:g.54325741=	NC_000004.11:g.54325741A>G
FIP1L1 RefSeqGene	NG_008644.1:g.86922=	NG_008644.1:g.86922A>G
FIP1L1 transcript variant 1	NM_030917.4:c.*125=	NM_030917.4:c.*125A>G
FIP1L1 transcript variant 1	NM_030917.3:c.*125=	NM_030917.3:c.*125A>G
FIP1L1 transcript variant 2	NM_001134937.2:c.*125=	NM_001134937.2:c.*125A>G
FIP1L1 transcript variant 2	NM_001134937.1:c.*125=	NM_001134937.1:c.*125A>G
FIP1L1 transcript variant 3	NM_001134938.2:c.*125=	NM_001134938.2:c.*125A>G
FIP1L1 transcript variant 3	NM_001134938.1:c.*125=	NM_001134938.1:c.*125A>G
FIP1L1 transcript variant 47	NR_164848.1:n.2227=	NR_164848.1:n.2227A>G
FIP1L1 transcript variant 4	NM_001376744.1:c.*125=	NM_001376744.1:c.*125A>G
FIP1L1 transcript variant 5	NM_001376745.1:c.*125=	NM_001376745.1:c.*125A>G
FIP1L1 transcript variant 6	NM_001376746.1:c.*125=	NM_001376746.1:c.*125A>G
FIP1L1 transcript variant 49	NM_001410723.1:c.*125=	NM_001410723.1:c.*125A>G
FIP1L1 transcript variant 8	NM_001376748.1:c.*125=	NM_001376748.1:c.*125A>G
FIP1L1 transcript variant 9	NM_001376749.1:c.*125=	NM_001376749.1:c.*125A>G
FIP1L1 transcript variant 10	NM_001376750.1:c.*125=	NM_001376750.1:c.*125A>G
FIP1L1 transcript variant 12	NM_001376752.1:c.*125=	NM_001376752.1:c.*125A>G
FIP1L1 transcript variant 11	NM_001376751.1:c.*125=	NM_001376751.1:c.*125A>G
FIP1L1 transcript variant 13	NM_001376753.1:c.*125=	NM_001376753.1:c.*125A>G
FIP1L1 transcript variant 14	NM_001376754.1:c.*125=	NM_001376754.1:c.*125A>G
FIP1L1 transcript variant 16	NM_001376756.1:c.*125=	NM_001376756.1:c.*125A>G
FIP1L1 transcript variant 15	NM_001376755.1:c.*125=	NM_001376755.1:c.*125A>G
FIP1L1 transcript variant 7	NM_001376747.1:c.*46=	NM_001376747.1:c.*46A>G
FIP1L1 transcript variant 18	NM_001376758.1:c.*125=	NM_001376758.1:c.*125A>G
FIP1L1 transcript variant 19	NM_001376759.1:c.*125=	NM_001376759.1:c.*125A>G
FIP1L1 transcript variant 21	NM_001376761.1:c.*125=	NM_001376761.1:c.*125A>G
FIP1L1 transcript variant 20	NM_001376760.1:c.*125=	NM_001376760.1:c.*125A>G
FIP1L1 transcript variant 48	NR_164849.1:n.2020=	NR_164849.1:n.2020A>G
FIP1L1 transcript variant 22	NM_001376762.1:c.*125=	NM_001376762.1:c.*125A>G
FIP1L1 transcript variant 23	NM_001376764.1:c.*125=	NM_001376764.1:c.*125A>G
FIP1L1 transcript variant 24	NM_001376765.1:c.*125=	NM_001376765.1:c.*125A>G
FIP1L1 transcript variant 26	NM_001376767.1:c.*125=	NM_001376767.1:c.*125A>G
FIP1L1 transcript variant 27	NM_001376768.1:c.*125=	NM_001376768.1:c.*125A>G
FIP1L1 transcript variant 28	NM_001376769.1:c.*125=	NM_001376769.1:c.*125A>G
FIP1L1 transcript variant 31	NM_001376772.1:c.*125=	NM_001376772.1:c.*125A>G
FIP1L1 transcript variant 30	NM_001376771.1:c.*125=	NM_001376771.1:c.*125A>G
FIP1L1 transcript variant 32	NM_001376773.1:c.*125=	NM_001376773.1:c.*125A>G
FIP1L1 transcript variant 17	NM_001376757.1:c.*46=	NM_001376757.1:c.*46A>G
FIP1L1 transcript variant 41	NM_001376782.1:c.*125=	NM_001376782.1:c.*125A>G
FIP1L1 transcript variant 33	NM_001376774.1:c.*125=	NM_001376774.1:c.*125A>G
FIP1L1 transcript variant 34	NM_001376775.1:c.*125=	NM_001376775.1:c.*125A>G
FIP1L1 transcript variant 46	NR_164847.1:n.1927=	NR_164847.1:n.1927A>G
FIP1L1 transcript variant 36	NM_001376777.1:c.*125=	NM_001376777.1:c.*125A>G
FIP1L1 transcript variant 37	NM_001376778.1:c.*125=	NM_001376778.1:c.*125A>G
FIP1L1 transcript variant 25	NM_001376766.1:c.*46=	NM_001376766.1:c.*46A>G
FIP1L1 transcript variant 38	NM_001376779.1:c.*125=	NM_001376779.1:c.*125A>G
FIP1L1 transcript variant 39	NM_001376780.1:c.*125=	NM_001376780.1:c.*125A>G
FIP1L1 transcript variant 40	NM_001376781.1:c.*125=	NM_001376781.1:c.*125A>G
FIP1L1 transcript variant 29	NM_001376770.1:c.*46=	NM_001376770.1:c.*46A>G
FIP1L1 transcript variant 42	NM_001376783.1:c.*125=	NM_001376783.1:c.*125A>G
FIP1L1 transcript variant 50	NM_001410724.1:c.*46=	NM_001410724.1:c.*46A>G
FIP1L1 transcript variant 44	NM_001376785.1:c.*125=	NM_001376785.1:c.*125A>G
FIP1L1 transcript variant 35	NM_001376776.1:c.*46=	NM_001376776.1:c.*46A>G
FIP1L1 transcript variant 43	NM_001376784.1:c.*46=	NM_001376784.1:c.*46A>G
FIP1L1 transcript variant 45	NM_001376786.1:c.*46=	NM_001376786.1:c.*46A>G
LNX1 transcript variant X2	XM_005265785.6:c.*1333=	XM_005265785.6:c.*1333T>C
LNX1 transcript variant X2	XM_005265785.4:c.*1333=	XM_005265785.4:c.*1333T>C
FIP1L1 transcript variant X7	XM_005265779.5:c.*46=	XM_005265779.5:c.*46A>G
FIP1L1 transcript variant X11	XM_005265779.4:c.*46=	XM_005265779.4:c.*46A>G
FIP1L1 transcript variant X12	XM_005265779.3:c.*46=	XM_005265779.3:c.*46A>G
FIP1L1 transcript variant X12	XM_005265779.2:c.*46=	XM_005265779.2:c.*46A>G
FIP1L1 transcript variant X12	XM_005265779.1:c.*46=	XM_005265779.1:c.*46A>G
LNX1 transcript variant 1	NM_001126328.3:c.*1333=	NM_001126328.3:c.*1333T>C
LNX1 transcript variant 2	NM_032622.3:c.*1333=	NM_032622.3:c.*1333T>C
LNX1 transcript variant X1	XM_024454262.2:c.*1333=	XM_024454262.2:c.*1333T>C
FIP1L1 transcript variant X1	XM_047416208.1:c.*125=	XM_047416208.1:c.*125A>G
FIP1L1 transcript variant X2	XM_047416209.1:c.*125=	XM_047416209.1:c.*125A>G
FIP1L1 transcript variant X2	XM_047416210.1:c.*125=	XM_047416210.1:c.*125A>G
FIP1L1 transcript variant X3	XM_047416211.1:c.*125=	XM_047416211.1:c.*125A>G
FIP1L1 transcript variant X4	XM_047416212.1:c.*125=	XM_047416212.1:c.*125A>G
FIP1L1 transcript variant X5	XM_047416213.1:c.*125=	XM_047416213.1:c.*125A>G
FIP1L1 transcript variant X6	XM_047416214.1:c.*125=	XM_047416214.1:c.*125A>G
FIP1L1 transcript variant X8	XM_047416215.1:c.*125=	XM_047416215.1:c.*125A>G
FIP1L1 transcript variant X9	XM_047416216.1:c.*125=	XM_047416216.1:c.*125A>G
FIP1L1 transcript variant X11	XM_047416217.1:c.*46=	XM_047416217.1:c.*46A>G
FIP1L1 transcript variant X10	XM_047416218.1:c.*46=	XM_047416218.1:c.*46A>G

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, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EVA_UK10K_ALSPAC	ss1610038585	Apr 01, 2015 (144)
2	EVA_UK10K_TWINSUK	ss1653032618	Apr 01, 2015 (144)
3	TOPMED	ss4613093986	Apr 26, 2021 (155)
4	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 54325741	Oct 12, 2018 (152)
5	TopMed	NC_000004.12 - 53459574	Apr 26, 2021 (155)
6	UK 10K study - Twins	NC_000004.11 - 54325741	Oct 12, 2018 (152)
7	ALFA	NC_000004.12 - 53459574	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
11707173, 11707173, ss1610038585, ss1653032618	NC_000004.11:54325740:A:G	NC_000004.12:53459573:A:G	(self)
450471542, 1624652902, ss4613093986	NC_000004.12:53459573:A:G	NC_000004.12:53459573:A:G	(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 rs772166980

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

rs772166980