Name: rs111874270
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.

rs111874270

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:88729081-88729082 (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: delC / dupC
Variation Type: Indel Insertion and Deletion
Frequency: delC=0.01210 (342/28258, 14KJPN)
delC=0.01080 (181/16756, 8.3KJPN)
delC=0.00193 (29/15008, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FAM13A-AS1 : Non Coding Transcript Variant
FAM13A : 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	HTRZ	HWEP
Total	Global	14958	CC=0.99806	C=0.00194, CCC=0.00000	0.996122	0.003878	0
European	Sub	11800	CC=0.99754	C=0.00246, CCC=0.00000	0.995085	0.004915	0
African	Sub	1832	CC=1.0000	C=0.0000, CCC=0.0000	1.0	0.0	N/A
African Others	Sub	66	CC=1.00	C=0.00, CCC=0.00	1.0	0.0	N/A
African American	Sub	1766	CC=1.0000	C=0.0000, CCC=0.0000	1.0	0.0	N/A
Asian	Sub	108	CC=1.000	C=0.000, CCC=0.000	1.0	0.0	N/A
East Asian	Sub	84	CC=1.00	C=0.00, CCC=0.00	1.0	0.0	N/A
Other Asian	Sub	24	CC=1.00	C=0.00, CCC=0.00	1.0	0.0	N/A
Latin American 1	Sub	132	CC=1.000	C=0.000, CCC=0.000	1.0	0.0	N/A
Latin American 2	Sub	590	CC=1.000	C=0.000, CCC=0.000	1.0	0.0	N/A
South Asian	Sub	92	CC=1.00	C=0.00, CCC=0.00	1.0	0.0	N/A
Other	Sub	404	CC=1.000	C=0.000, CCC=0.000	1.0	0.0	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
14KJPN	JAPANESE	Study-wide	28258	CC=0.98790	delC=0.01210
8.3KJPN	JAPANESE	Study-wide	16756	CC=0.98920	delC=0.01080
Allele Frequency Aggregator	Total	Global	15008	CC=0.99640	delC=0.00193, dupC=0.00000
Allele Frequency Aggregator	European	Sub	11850	CC=0.99544	delC=0.00245, dupC=0.00000
Allele Frequency Aggregator	African	Sub	1832	CC=1.0000	delC=0.0000, dupC=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	590	CC=1.000	delC=0.000, dupC=0.000
Allele Frequency Aggregator	Other	Sub	404	CC=1.000	delC=0.000, dupC=0.000
Allele Frequency Aggregator	Latin American 1	Sub	132	CC=1.000	delC=0.000, dupC=0.000
Allele Frequency Aggregator	Asian	Sub	108	CC=1.000	delC=0.000, dupC=0.000
Allele Frequency Aggregator	South Asian	Sub	92	CC=1.00	delC=0.00, dupC=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 4	NC_000004.12:g.88729082del
GRCh38.p14 chr 4	NC_000004.12:g.88729082dup
GRCh37.p13 chr 4	NC_000004.11:g.89650233del
GRCh37.p13 chr 4	NC_000004.11:g.89650233dup

Gene: FAM13A, family with sequence similarity 13 member A (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FAM13A transcript variant 2	NM_001015045.3:c.1968-422… NM_001015045.3:c.1968-422del	N/A	Intron Variant
FAM13A transcript variant 3	NM_001265578.2:c.1926-422… NM_001265578.2:c.1926-422del	N/A	Intron Variant
FAM13A transcript variant 4	NM_001265579.2:c.1884-422… NM_001265579.2:c.1884-422del	N/A	Intron Variant
FAM13A transcript variant 5	NM_001265580.2:c.1884-422… NM_001265580.2:c.1884-422del	N/A	Intron Variant
FAM13A transcript variant 1	NM_014883.4:c.2946-422del	N/A	Intron Variant
FAM13A transcript variant X4	XM_005262683.4:c.2862-422… XM_005262683.4:c.2862-422del	N/A	Intron Variant
FAM13A transcript variant X14	XM_006714057.4:c.2379-422… XM_006714057.4:c.2379-422del	N/A	Intron Variant
FAM13A transcript variant X1	XM_011531516.2:c.2946-422… XM_011531516.2:c.2946-422del	N/A	Intron Variant
FAM13A transcript variant X3	XM_011531517.3:c.2862-422… XM_011531517.3:c.2862-422del	N/A	Intron Variant
FAM13A transcript variant X12	XM_011531518.2:c.2388-422… XM_011531518.2:c.2388-422del	N/A	Intron Variant
FAM13A transcript variant X11	XM_011531519.4:c.2388-422… XM_011531519.4:c.2388-422del	N/A	Intron Variant
FAM13A transcript variant X5	XM_017007624.3:c.2820-422… XM_017007624.3:c.2820-422del	N/A	Intron Variant
FAM13A transcript variant X7	XM_017007625.1:c.2781-422… XM_017007625.1:c.2781-422del	N/A	Intron Variant
FAM13A transcript variant X10	XM_017007626.1:c.2415-422… XM_017007626.1:c.2415-422del	N/A	Intron Variant
FAM13A transcript variant X17	XM_017007633.3:c.1983-422… XM_017007633.3:c.1983-422del	N/A	Intron Variant
FAM13A transcript variant X18	XM_017007634.3:c.1842-422… XM_017007634.3:c.1842-422del	N/A	Intron Variant
FAM13A transcript variant X2	XM_047449479.1:c.2904-422… XM_047449479.1:c.2904-422del	N/A	Intron Variant
FAM13A transcript variant X6	XM_047449480.1:c.2820-422… XM_047449480.1:c.2820-422del	N/A	Intron Variant
FAM13A transcript variant X8	XM_047449481.1:c.2778-422… XM_047449481.1:c.2778-422del	N/A	Intron Variant
FAM13A transcript variant X9	XM_047449482.1:c.2736-422… XM_047449482.1:c.2736-422del	N/A	Intron Variant
FAM13A transcript variant X13	XM_047449483.1:c.2388-422… XM_047449483.1:c.2388-422del	N/A	Intron Variant
FAM13A transcript variant X15	XM_047449484.1:c.2130-422… XM_047449484.1:c.2130-422del	N/A	Intron Variant
FAM13A transcript variant X16	XM_047449485.1:c.2130-422… XM_047449485.1:c.2130-422del	N/A	Intron Variant
FAM13A transcript variant X19	XM_047449487.1:c.1800-422… XM_047449487.1:c.1800-422del	N/A	Intron Variant

Gene: FAM13A-AS1, FAM13A antisense RNA 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FAM13A-AS1 transcript	NR_002806.2:n.2189del	N/A	Non Coding Transcript Variant
FAM13A-AS1 transcript	NR_002806.2:n.2189dup	N/A	Non Coding 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	CC=	delC	dupC
GRCh38.p14 chr 4	NC_000004.12:g.88729081_88729082=	NC_000004.12:g.88729082del	NC_000004.12:g.88729082dup
GRCh37.p13 chr 4	NC_000004.11:g.89650232_89650233=	NC_000004.11:g.89650233del	NC_000004.11:g.89650233dup
FAM13A-AS1 transcript	NR_002806.2:n.2188_2189=	NR_002806.2:n.2189del	NR_002806.2:n.2189dup
FAM13A transcript variant 2	NM_001015045.2:c.1968-422=	NM_001015045.2:c.1968-422del	NM_001015045.2:c.1968-422dup
FAM13A transcript variant 2	NM_001015045.3:c.1968-422=	NM_001015045.3:c.1968-422del	NM_001015045.3:c.1968-422dup
FAM13A transcript variant 3	NM_001265578.1:c.1926-422=	NM_001265578.1:c.1926-422del	NM_001265578.1:c.1926-422dup
FAM13A transcript variant 3	NM_001265578.2:c.1926-422=	NM_001265578.2:c.1926-422del	NM_001265578.2:c.1926-422dup
FAM13A transcript variant 4	NM_001265579.1:c.1884-422=	NM_001265579.1:c.1884-422del	NM_001265579.1:c.1884-422dup
FAM13A transcript variant 4	NM_001265579.2:c.1884-422=	NM_001265579.2:c.1884-422del	NM_001265579.2:c.1884-422dup
FAM13A transcript variant 5	NM_001265580.1:c.1884-422=	NM_001265580.1:c.1884-422del	NM_001265580.1:c.1884-422dup
FAM13A transcript variant 5	NM_001265580.2:c.1884-422=	NM_001265580.2:c.1884-422del	NM_001265580.2:c.1884-422dup
FAM13A transcript variant 1	NM_014883.3:c.2946-422=	NM_014883.3:c.2946-422del	NM_014883.3:c.2946-422dup
FAM13A transcript variant 1	NM_014883.4:c.2946-422=	NM_014883.4:c.2946-422del	NM_014883.4:c.2946-422dup
FAM13A transcript variant X1	XM_005262681.1:c.2904-422=	XM_005262681.1:c.2904-422del	XM_005262681.1:c.2904-422dup
FAM13A transcript variant X2	XM_005262682.1:c.2886-422=	XM_005262682.1:c.2886-422del	XM_005262682.1:c.2886-422dup
FAM13A transcript variant X3	XM_005262683.1:c.2862-422=	XM_005262683.1:c.2862-422del	XM_005262683.1:c.2862-422dup
FAM13A transcript variant X4	XM_005262683.4:c.2862-422=	XM_005262683.4:c.2862-422del	XM_005262683.4:c.2862-422dup
FAM13A transcript variant X4	XM_005262684.1:c.2319-422=	XM_005262684.1:c.2319-422del	XM_005262684.1:c.2319-422dup
FAM13A transcript variant X14	XM_006714057.4:c.2379-422=	XM_006714057.4:c.2379-422del	XM_006714057.4:c.2379-422dup
FAM13A transcript variant X1	XM_011531516.2:c.2946-422=	XM_011531516.2:c.2946-422del	XM_011531516.2:c.2946-422dup
FAM13A transcript variant X3	XM_011531517.3:c.2862-422=	XM_011531517.3:c.2862-422del	XM_011531517.3:c.2862-422dup
FAM13A transcript variant X12	XM_011531518.2:c.2388-422=	XM_011531518.2:c.2388-422del	XM_011531518.2:c.2388-422dup
FAM13A transcript variant X11	XM_011531519.4:c.2388-422=	XM_011531519.4:c.2388-422del	XM_011531519.4:c.2388-422dup
FAM13A transcript variant X5	XM_017007624.3:c.2820-422=	XM_017007624.3:c.2820-422del	XM_017007624.3:c.2820-422dup
FAM13A transcript variant X7	XM_017007625.1:c.2781-422=	XM_017007625.1:c.2781-422del	XM_017007625.1:c.2781-422dup
FAM13A transcript variant X10	XM_017007626.1:c.2415-422=	XM_017007626.1:c.2415-422del	XM_017007626.1:c.2415-422dup
FAM13A transcript variant X17	XM_017007633.3:c.1983-422=	XM_017007633.3:c.1983-422del	XM_017007633.3:c.1983-422dup
FAM13A transcript variant X18	XM_017007634.3:c.1842-422=	XM_017007634.3:c.1842-422del	XM_017007634.3:c.1842-422dup
FAM13A transcript variant X2	XM_047449479.1:c.2904-422=	XM_047449479.1:c.2904-422del	XM_047449479.1:c.2904-422dup
FAM13A transcript variant X6	XM_047449480.1:c.2820-422=	XM_047449480.1:c.2820-422del	XM_047449480.1:c.2820-422dup
FAM13A transcript variant X8	XM_047449481.1:c.2778-422=	XM_047449481.1:c.2778-422del	XM_047449481.1:c.2778-422dup
FAM13A transcript variant X9	XM_047449482.1:c.2736-422=	XM_047449482.1:c.2736-422del	XM_047449482.1:c.2736-422dup
FAM13A transcript variant X13	XM_047449483.1:c.2388-422=	XM_047449483.1:c.2388-422del	XM_047449483.1:c.2388-422dup
FAM13A transcript variant X15	XM_047449484.1:c.2130-422=	XM_047449484.1:c.2130-422del	XM_047449484.1:c.2130-422dup
FAM13A transcript variant X16	XM_047449485.1:c.2130-422=	XM_047449485.1:c.2130-422del	XM_047449485.1:c.2130-422dup
FAM13A transcript variant X19	XM_047449487.1:c.1800-422=	XM_047449487.1:c.1800-422del	XM_047449487.1:c.1800-422dup

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#.

14 SubSNP, 5 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BUSHMAN	ss193748853	Jul 04, 2010 (132)
2	EVA_DECODE	ss1589869075	Apr 01, 2015 (144)
3	SWEGEN	ss2995087930	Nov 08, 2017 (151)
4	EVA_DECODE	ss3712511663	Jul 13, 2019 (153)
5	EVA	ss3828666048	Apr 26, 2020 (154)
6	GNOMAD	ss4115408934	Apr 26, 2021 (155)
7	TOMMO_GENOMICS	ss5166755724	Apr 26, 2021 (155)
8	1000G_HIGH_COVERAGE	ss5260027970	Oct 17, 2022 (156)
9	HUGCELL_USP	ss5458698615	Oct 17, 2022 (156)
10	SANFORD_IMAGENETICS	ss5635515315	Oct 17, 2022 (156)
11	TOMMO_GENOMICS	ss5701395407	Oct 17, 2022 (156)
12	YY_MCH	ss5805291237	Oct 17, 2022 (156)
13	EVA	ss5844319984	Oct 17, 2022 (156)
14	EVA	ss5864382919	Oct 17, 2022 (156)
15	gnomAD - Genomes Submission ignored due to conflicting rows: Row 156630896 (NC_000004.12:88729080::C 2/132982) Row 156630898 (NC_000004.12:88729080:C: 7736/132716)	-	Apr 26, 2021 (155)
16	gnomAD - Genomes Submission ignored due to conflicting rows: Row 156630896 (NC_000004.12:88729080::C 2/132982) Row 156630898 (NC_000004.12:88729080:C: 7736/132716)	-	Apr 26, 2021 (155)
17	8.3KJPN	NC_000004.11 - 89650232	Apr 26, 2021 (155)
18	14KJPN	NC_000004.12 - 88729081	Oct 17, 2022 (156)
19	ALFA	NC_000004.12 - 88729081	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
ss1589869075	NC_000004.10:89869254:C:	NC_000004.12:88729080:CC:C	(self)
24725031, ss2995087930, ss3828666048, ss5166755724, ss5635515315, ss5844319984	NC_000004.11:89650231:C:	NC_000004.12:88729080:CC:C	(self)
35232511, ss5260027970, ss5458698615, ss5701395407, ss5805291237, ss5864382919	NC_000004.12:88729080:C:	NC_000004.12:88729080:CC:C	(self)
11510062482	NC_000004.12:88729080:CC:C	NC_000004.12:88729080:CC:C	(self)
ss3712511663	NC_000004.12:88729081:C:	NC_000004.12:88729080:CC:C	(self)
ss193748853	NT_016354.20:29807700:C:	NC_000004.12:88729080:CC:C	(self)
ss4115408934	NC_000004.12:88729080::C	NC_000004.12:88729080:CC:CCC	(self)
11510062482	NC_000004.12:88729080:CC:CCC	NC_000004.12:88729080:CC:CCC	(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 rs111874270

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
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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

rs111874270