Name: rs374509897
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.

rs374509897

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:51629960 (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: G=0.00071 (23/32314, GnomAD)
G=0.01120 (312/27864, 14KJPN)
G=0.00013 (3/23132, ALFA) (+ 6 more)
G=0.01090 (180/16518, 8.3KJPN)
G=0.00033 (4/12034, GO-ESP)
G=0.0044 (28/6404, 1000G_30x)
G=0.0054 (27/5008, 1000G)
G=0.0217 (61/2808, KOREAN)
G=0.0143 (25/1750, Korea1K)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SIGLEC5 : Missense 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	23132	C=0.99987	G=0.00013
European	Sub	15684	C=1.00000	G=0.00000
African	Sub	3524	C=0.9997	G=0.0003
African Others	Sub	122	C=1.000	G=0.000
African American	Sub	3402	C=0.9997	G=0.0003
Asian	Sub	168	C=0.994	G=0.006
East Asian	Sub	112	C=1.000	G=0.000
Other Asian	Sub	56	C=0.98	G=0.02
Latin American 1	Sub	146	C=1.000	G=0.000
Latin American 2	Sub	610	C=1.000	G=0.000
South Asian	Sub	98	C=1.00	G=0.00
Other	Sub	2902	C=0.9997	G=0.0003

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
gnomAD - Genomes	Global	Study-wide	32314	C=0.99929	G=0.00071
gnomAD - Genomes	European	Sub	17270	C=1.00000	G=0.00000
gnomAD - Genomes	African	Sub	10596	C=0.99924	G=0.00076
gnomAD - Genomes	American	Sub	1916	C=0.9995	G=0.0005
gnomAD - Genomes	East Asian	Sub	1268	C=0.9897	G=0.0103
gnomAD - Genomes	Ashkenazi Jewish	Sub	852	C=1.000	G=0.000
gnomAD - Genomes	Other	Sub	412	C=0.998	G=0.002
14KJPN	JAPANESE	Study-wide	27864	C=0.98880	G=0.01120
Allele Frequency Aggregator	Total	Global	23132	C=0.99987	G=0.00013
Allele Frequency Aggregator	European	Sub	15684	C=1.00000	G=0.00000
Allele Frequency Aggregator	African	Sub	3524	C=0.9997	G=0.0003
Allele Frequency Aggregator	Other	Sub	2902	C=0.9997	G=0.0003
Allele Frequency Aggregator	Latin American 2	Sub	610	C=1.000	G=0.000
Allele Frequency Aggregator	Asian	Sub	168	C=0.994	G=0.006
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	G=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	G=0.00
8.3KJPN	JAPANESE	Study-wide	16518	C=0.98910	G=0.01090
GO Exome Sequencing Project	Global	Study-wide	12034	C=0.99967	G=0.00033
GO Exome Sequencing Project	European American	Sub	7970	C=1.0000	G=0.0000
GO Exome Sequencing Project	African American	Sub	4064	C=0.9990	G=0.0010
1000Genomes_30x	Global	Study-wide	6404	C=0.9956	G=0.0044
1000Genomes_30x	African	Sub	1786	C=1.0000	G=0.0000
1000Genomes_30x	Europe	Sub	1266	C=1.0000	G=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	G=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.9761	G=0.0239
1000Genomes_30x	American	Sub	980	C=1.000	G=0.000
1000Genomes	Global	Study-wide	5008	C=0.9946	G=0.0054
1000Genomes	African	Sub	1322	C=1.0000	G=0.0000
1000Genomes	East Asian	Sub	1008	C=0.9732	G=0.0268
1000Genomes	Europe	Sub	1006	C=1.0000	G=0.0000
1000Genomes	South Asian	Sub	978	C=1.000	G=0.000
1000Genomes	American	Sub	694	C=1.000	G=0.000
KOREAN population from KRGDB	KOREAN	Study-wide	2808	C=0.9783	G=0.0217
Korean Genome Project	KOREAN	Study-wide	1750	C=0.9857	G=0.0143

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 19	NC_000019.10:g.51629960C>G
GRCh38.p14 chr 19	NC_000019.10:g.51629960C>T
GRCh37.p13 chr 19	NC_000019.9:g.52133213C>G
GRCh37.p13 chr 19	NC_000019.9:g.52133213C>T

Gene: SIGLEC5, sialic acid binding Ig like lectin 5 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SIGLEC5 transcript variant 1	NM_003830.4:c.294G>C	K [AAG] > N [AAC]	Coding Sequence Variant
sialic acid-binding Ig-like lectin 5 isoform 1 precursor	NP_003821.1:p.Lys98Asn	K (Lys) > N (Asn)	Missense Variant
SIGLEC5 transcript variant 1	NM_003830.4:c.294G>A	K [AAG] > K [AAA]	Coding Sequence Variant
sialic acid-binding Ig-like lectin 5 isoform 1 precursor	NP_003821.1:p.Lys98=	K (Lys) > K (Lys)	Synonymous Variant
SIGLEC5 transcript variant 2	NM_001384708.1:c.294G>C	K [AAG] > N [AAC]	Coding Sequence Variant
sialic acid-binding Ig-like lectin 5 isoform 2 precursor	NP_001371637.1:p.Lys98Asn	K (Lys) > N (Asn)	Missense Variant
SIGLEC5 transcript variant 2	NM_001384708.1:c.294G>A	K [AAG] > K [AAA]	Coding Sequence Variant
sialic acid-binding Ig-like lectin 5 isoform 2 precursor	NP_001371637.1:p.Lys98=	K (Lys) > K (Lys)	Synonymous Variant
SIGLEC5 transcript variant 3	NM_001384709.1:c.294G>C	K [AAG] > N [AAC]	Coding Sequence Variant
sialic acid-binding Ig-like lectin 5 isoform 3 precursor	NP_001371638.1:p.Lys98Asn	K (Lys) > N (Asn)	Missense Variant
SIGLEC5 transcript variant 3	NM_001384709.1:c.294G>A	K [AAG] > K [AAA]	Coding Sequence Variant
sialic acid-binding Ig-like lectin 5 isoform 3 precursor	NP_001371638.1:p.Lys98=	K (Lys) > K (Lys)	Synonymous 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 19	NC_000019.10:g.51629960=	NC_000019.10:g.51629960C>G	NC_000019.10:g.51629960C>T
GRCh37.p13 chr 19	NC_000019.9:g.52133213=	NC_000019.9:g.52133213C>G	NC_000019.9:g.52133213C>T
SIGLEC5 transcript variant 1	NM_003830.4:c.294=	NM_003830.4:c.294G>C	NM_003830.4:c.294G>A
SIGLEC5 transcript	NM_003830.3:c.294=	NM_003830.3:c.294G>C	NM_003830.3:c.294G>A
SIGLEC5 transcript variant 2	NM_001384708.1:c.294=	NM_001384708.1:c.294G>C	NM_001384708.1:c.294G>A
SIGLEC5 transcript variant 3	NM_001384709.1:c.294=	NM_001384709.1:c.294G>C	NM_001384709.1:c.294G>A
sialic acid-binding Ig-like lectin 5 isoform 1 precursor	NP_003821.1:p.Lys98=	NP_003821.1:p.Lys98Asn	NP_003821.1:p.Lys98=
sialic acid-binding Ig-like lectin 5 isoform 2 precursor	NP_001371637.1:p.Lys98=	NP_001371637.1:p.Lys98Asn	NP_001371637.1:p.Lys98=
sialic acid-binding Ig-like lectin 5 isoform 3 precursor	NP_001371638.1:p.Lys98=	NP_001371638.1:p.Lys98Asn	NP_001371638.1:p.Lys98=

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#.

18 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	NHLBI-ESP	ss713533534	Apr 25, 2013 (138)
2	1000GENOMES	ss1363533491	Aug 21, 2014 (142)
3	EVA_EXAC	ss1693767222	Apr 01, 2015 (144)
4	EVA_EXAC	ss1693767223	Apr 01, 2015 (144)
5	GNOMAD	ss2744253603	Nov 08, 2017 (151)
6	GNOMAD	ss2750270742	Nov 08, 2017 (151)
7	GNOMAD	ss2963941945	Nov 08, 2017 (151)
8	KHV_HUMAN_GENOMES	ss3821423384	Jul 13, 2019 (153)
9	EVA	ss3825322213	Apr 27, 2020 (154)
10	KRGDB	ss3938580856	Apr 27, 2020 (154)
11	KOGIC	ss3981565843	Apr 27, 2020 (154)
12	TOMMO_GENOMICS	ss5228214368	Apr 26, 2021 (155)
13	EVA	ss5236965090	Apr 26, 2021 (155)
14	1000G_HIGH_COVERAGE	ss5307595072	Oct 13, 2022 (156)
15	EVA	ss5435417960	Oct 13, 2022 (156)
16	1000G_HIGH_COVERAGE	ss5613466711	Oct 13, 2022 (156)
17	TOMMO_GENOMICS	ss5787003083	Oct 13, 2022 (156)
18	YY_MCH	ss5817683677	Oct 13, 2022 (156)
19	1000Genomes	NC_000019.9 - 52133213	Oct 12, 2018 (152)
20	1000Genomes_30x	NC_000019.10 - 51629960	Oct 13, 2022 (156)
21	ExAC Submission ignored due to conflicting rows: Row 4283677 (NC_000019.9:52133212:C:C 79790/79970, NC_000019.9:52133212:C:G 180/79970) Row 4283678 (NC_000019.9:52133212:C:C 79968/79970, NC_000019.9:52133212:C:T 2/79970)	-	Oct 12, 2018 (152)
22	ExAC Submission ignored due to conflicting rows: Row 4283677 (NC_000019.9:52133212:C:C 79790/79970, NC_000019.9:52133212:C:G 180/79970) Row 4283678 (NC_000019.9:52133212:C:C 79968/79970, NC_000019.9:52133212:C:T 2/79970)	-	Oct 12, 2018 (152)
23	gnomAD - Genomes	NC_000019.10 - 51629960	Apr 26, 2021 (155)
24	gnomAD - Exomes Submission ignored due to conflicting rows: Row 13567211 (NC_000019.9:52133212:C:C 198917/199306, NC_000019.9:52133212:C:G 389/199306) Row 13567212 (NC_000019.9:52133212:C:C 199303/199306, NC_000019.9:52133212:C:T 3/199306)	-	Jul 13, 2019 (153)
25	gnomAD - Exomes Submission ignored due to conflicting rows: Row 13567211 (NC_000019.9:52133212:C:C 198917/199306, NC_000019.9:52133212:C:G 389/199306) Row 13567212 (NC_000019.9:52133212:C:C 199303/199306, NC_000019.9:52133212:C:T 3/199306)	-	Jul 13, 2019 (153)
26	GO Exome Sequencing Project	NC_000019.9 - 52133213	Oct 12, 2018 (152)
27	KOREAN population from KRGDB	NC_000019.9 - 52133213	Apr 27, 2020 (154)
28	Korean Genome Project	NC_000019.10 - 51629960	Apr 27, 2020 (154)
29	8.3KJPN	NC_000019.9 - 52133213	Apr 26, 2021 (155)
30	14KJPN	NC_000019.10 - 51629960	Oct 13, 2022 (156)
31	ALFA	NC_000019.10 - 51629960	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
76954033, 1779150, 45758250, 86183675, ss713533534, ss1363533491, ss1693767222, ss2744253603, ss2750270742, ss2963941945, ss3825322213, ss3938580856, ss5228214368, ss5435417960	NC_000019.9:52133212:C:G	NC_000019.10:51629959:C:G	(self)
100992646, 542717645, 37943844, 120840187, 8668758284, ss3821423384, ss3981565843, ss5236965090, ss5307595072, ss5613466711, ss5787003083, ss5817683677	NC_000019.10:51629959:C:G	NC_000019.10:51629959:C:G	(self)
ss1693767223, ss2744253603	NC_000019.9:52133212:C:T	NC_000019.10:51629959: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 rs374509897

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

rs374509897