Name: rs77822621
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.

rs77822621

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:1014424 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.02011 (829/41226, ALFA)
T=0.0089 (57/6404, 1000G_30x)
T=0.0088 (44/5008, 1000G) (+ 9 more)
T=0.0176 (79/4480, Estonian)
T=0.0397 (153/3854, ALSPAC)
T=0.0361 (134/3708, TWINSUK)
T=0.033 (33/998, GoNL)
T=0.037 (22/600, NorthernSweden)
T=0.005 (1/216, Qatari)
T=0.05 (2/40, GENOME_DK)
C=0.5 (4/8, SGDP_PRJ)
T=0.5 (4/8, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FGFRL1 : 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	41226	C=0.97989	G=0.00000, T=0.02011
European	Sub	33096	C=0.97894	G=0.00000, T=0.02106
African	Sub	2936	C=1.0000	G=0.0000, T=0.0000
African Others	Sub	114	C=1.000	G=0.000, T=0.000
African American	Sub	2822	C=1.0000	G=0.0000, T=0.0000
Asian	Sub	116	C=1.000	G=0.000, T=0.000
East Asian	Sub	88	C=1.00	G=0.00, T=0.00
Other Asian	Sub	28	C=1.00	G=0.00, T=0.00
Latin American 1	Sub	150	C=0.993	G=0.000, T=0.007
Latin American 2	Sub	592	C=1.000	G=0.000, T=0.000
South Asian	Sub	98	C=1.00	G=0.00, T=0.00
Other	Sub	4238	C=0.9691	G=0.0000, T=0.0309

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
Allele Frequency Aggregator	Total	Global	41226	C=0.97989	G=0.00000, T=0.02011
Allele Frequency Aggregator	European	Sub	33096	C=0.97894	G=0.00000, T=0.02106
Allele Frequency Aggregator	Other	Sub	4238	C=0.9691	G=0.0000, T=0.0309
Allele Frequency Aggregator	African	Sub	2936	C=1.0000	G=0.0000, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	592	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	150	C=0.993	G=0.000, T=0.007
Allele Frequency Aggregator	Asian	Sub	116	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	G=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.9911	T=0.0089
1000Genomes_30x	African	Sub	1786	C=0.9994	T=0.0006
1000Genomes_30x	Europe	Sub	1266	C=0.9652	T=0.0348
1000Genomes_30x	South Asian	Sub	1202	C=0.9992	T=0.0008
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.989	T=0.011
1000Genomes	Global	Study-wide	5008	C=0.9912	T=0.0088
1000Genomes	African	Sub	1322	C=0.9992	T=0.0008
1000Genomes	East Asian	Sub	1008	C=0.9980	T=0.0020
1000Genomes	Europe	Sub	1006	C=0.9692	T=0.0308
1000Genomes	South Asian	Sub	978	C=0.999	T=0.001
1000Genomes	American	Sub	694	C=0.987	T=0.013
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9824	T=0.0176
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9603	T=0.0397
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9639	T=0.0361
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.967	T=0.033
Northern Sweden	ACPOP	Study-wide	600	C=0.963	T=0.037
Qatari	Global	Study-wide	216	C=0.995	T=0.005
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
SGDP_PRJ	Global	Study-wide	8	C=0.5	T=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 4	NC_000004.12:g.1014424C>G
GRCh38.p14 chr 4	NC_000004.12:g.1014424C>T
GRCh37.p13 chr 4	NC_000004.11:g.1008212C>G
GRCh37.p13 chr 4	NC_000004.11:g.1008212C>T

Gene: FGFRL1, fibroblast growth factor receptor like 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FGFRL1 transcript variant 1	NM_001004356.3:c.79+1860C… NM_001004356.3:c.79+1860C>G	N/A	Intron Variant
FGFRL1 transcript variant 2	NM_001004358.1:c.79+1860C… NM_001004358.1:c.79+1860C>G	N/A	Intron Variant
FGFRL1 transcript variant 4	NM_001370296.1:c.79+1860C… NM_001370296.1:c.79+1860C>G	N/A	Intron Variant
FGFRL1 transcript variant 3	NM_021923.3:c.79+1860C>G	N/A	Intron Variant
FGFRL1 transcript variant X1	XM_024454092.2:c.148+1860… XM_024454092.2:c.148+1860C>G	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	C=	G	T
GRCh38.p14 chr 4	NC_000004.12:g.1014424=	NC_000004.12:g.1014424C>G	NC_000004.12:g.1014424C>T
GRCh37.p13 chr 4	NC_000004.11:g.1008212=	NC_000004.11:g.1008212C>G	NC_000004.11:g.1008212C>T
FGFRL1 transcript variant 1	NM_001004356.2:c.79+1860=	NM_001004356.2:c.79+1860C>G	NM_001004356.2:c.79+1860C>T
FGFRL1 transcript variant 1	NM_001004356.3:c.79+1860=	NM_001004356.3:c.79+1860C>G	NM_001004356.3:c.79+1860C>T
FGFRL1 transcript variant 2	NM_001004358.1:c.79+1860=	NM_001004358.1:c.79+1860C>G	NM_001004358.1:c.79+1860C>T
FGFRL1 transcript variant 4	NM_001370296.1:c.79+1860=	NM_001370296.1:c.79+1860C>G	NM_001370296.1:c.79+1860C>T
FGFRL1 transcript variant 3	NM_021923.3:c.79+1860=	NM_021923.3:c.79+1860C>G	NM_021923.3:c.79+1860C>T
FGFRL1 transcript variant X1	XM_005272281.1:c.79+1860=	XM_005272281.1:c.79+1860C>G	XM_005272281.1:c.79+1860C>T
FGFRL1 transcript variant X2	XM_005272282.1:c.79+1860=	XM_005272282.1:c.79+1860C>G	XM_005272282.1:c.79+1860C>T
FGFRL1 transcript variant X1	XM_024454092.2:c.148+1860=	XM_024454092.2:c.148+1860C>G	XM_024454092.2:c.148+1860C>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#.

36 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss232223207	Jul 14, 2010 (132)
2	ILLUMINA	ss535753615	Sep 08, 2015 (146)
3	EVA-GONL	ss979667389	Aug 21, 2014 (142)
4	1000GENOMES	ss1308066251	Aug 21, 2014 (142)
5	EVA_GENOME_DK	ss1580378317	Apr 01, 2015 (144)
6	EVA_DECODE	ss1589164071	Apr 01, 2015 (144)
7	EVA_UK10K_ALSPAC	ss1609225460	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1652219493	Apr 01, 2015 (144)
9	WEILL_CORNELL_DGM	ss1922897445	Feb 12, 2016 (147)
10	GENOMED	ss1969636377	Jul 19, 2016 (147)
11	JJLAB	ss2022022827	Sep 14, 2016 (149)
12	HUMAN_LONGEVITY	ss2259778009	Dec 20, 2016 (150)
13	GNOMAD	ss2804624262	Nov 08, 2017 (151)
14	SWEGEN	ss2993983337	Nov 08, 2017 (151)
15	CSHL	ss3345495456	Nov 08, 2017 (151)
16	ILLUMINA	ss3628882844	Oct 12, 2018 (152)
17	EGCUT_WGS	ss3661922210	Jul 13, 2019 (153)
18	EVA_DECODE	ss3711224908	Jul 13, 2019 (153)
19	ACPOP	ss3730773334	Jul 13, 2019 (153)
20	ILLUMINA	ss3744521425	Jul 13, 2019 (153)
21	EVA	ss3828323212	Apr 25, 2020 (154)
22	SGDP_PRJ	ss3858009696	Apr 25, 2020 (154)
23	TOPMED	ss4599995121	Apr 26, 2021 (155)
24	TOPMED	ss4599995122	Apr 26, 2021 (155)
25	1000G_HIGH_COVERAGE	ss5257721843	Oct 17, 2022 (156)
26	EVA	ss5346335555	Oct 17, 2022 (156)
27	HUGCELL_USP	ss5456679642	Oct 17, 2022 (156)
28	EVA	ss5507366410	Oct 17, 2022 (156)
29	1000G_HIGH_COVERAGE	ss5538011709	Oct 17, 2022 (156)
30	SANFORD_IMAGENETICS	ss5624544873	Oct 17, 2022 (156)
31	SANFORD_IMAGENETICS	ss5634162514	Oct 17, 2022 (156)
32	EVA	ss5843420387	Oct 17, 2022 (156)
33	EVA	ss5847998200	Oct 17, 2022 (156)
34	EVA	ss5861793902	Oct 17, 2022 (156)
35	EVA	ss5962538375	Oct 17, 2022 (156)
36	EVA	ss5979687523	Oct 17, 2022 (156)
37	1000Genomes	NC_000004.11 - 1008212	Oct 12, 2018 (152)
38	1000Genomes_30x	NC_000004.12 - 1014424	Oct 17, 2022 (156)
39	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 1008212	Oct 12, 2018 (152)
40	Genetic variation in the Estonian population	NC_000004.11 - 1008212	Oct 12, 2018 (152)
41	The Danish reference pan genome	NC_000004.11 - 1008212	Apr 25, 2020 (154)
42	gnomAD - Genomes Submission ignored due to conflicting rows: Row 137750131 (NC_000004.12:1014423:C:G 1/140254) Row 137750132 (NC_000004.12:1014423:C:T 3308/140250)	-	Apr 26, 2021 (155)
43	gnomAD - Genomes Submission ignored due to conflicting rows: Row 137750131 (NC_000004.12:1014423:C:G 1/140254) Row 137750132 (NC_000004.12:1014423:C:T 3308/140250)	-	Apr 26, 2021 (155)
44	Genome of the Netherlands Release 5	NC_000004.11 - 1008212	Apr 25, 2020 (154)
45	Northern Sweden	NC_000004.11 - 1008212	Jul 13, 2019 (153)
46	Qatari	NC_000004.11 - 1008212	Apr 25, 2020 (154)
47	SGDP_PRJ	NC_000004.11 - 1008212	Apr 25, 2020 (154)
48	TopMed Submission ignored due to conflicting rows: Row 437372677 (NC_000004.12:1014423:C:G 3/264690) Row 437372678 (NC_000004.12:1014423:C:T 6467/264690)	-	Apr 26, 2021 (155)
49	TopMed Submission ignored due to conflicting rows: Row 437372677 (NC_000004.12:1014423:C:G 3/264690) Row 437372678 (NC_000004.12:1014423:C:T 6467/264690)	-	Apr 26, 2021 (155)
50	UK 10K study - Twins	NC_000004.11 - 1008212	Oct 12, 2018 (152)
51	ALFA	NC_000004.12 - 1014424	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
ss2804624262	NC_000004.11:1008211:C:G	NC_000004.12:1014423:C:G	(self)
6788056822, ss4599995121	NC_000004.12:1014423:C:G	NC_000004.12:1014423:C:G	(self)
ss1589164071	NC_000004.10:998211:C:T	NC_000004.12:1014423:C:T	(self)
19403487, 10816580, 7660458, 6543256, 4754410, 4058199, 4939375, 10026676, 10816580, ss232223207, ss535753615, ss979667389, ss1308066251, ss1580378317, ss1609225460, ss1652219493, ss1922897445, ss1969636377, ss2022022827, ss2804624262, ss2993983337, ss3345495456, ss3628882844, ss3661922210, ss3730773334, ss3744521425, ss3828323212, ss3858009696, ss5346335555, ss5507366410, ss5624544873, ss5634162514, ss5843420387, ss5847998200, ss5962538375, ss5979687523	NC_000004.11:1008211:C:T	NC_000004.12:1014423:C:T	(self)
25537644, 6788056822, ss2259778009, ss3711224908, ss4599995122, ss5257721843, ss5456679642, ss5538011709, ss5861793902	NC_000004.12:1014423:C:T	NC_000004.12:1014423: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 rs77822621

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

rs77822621