Name: rs140336145
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.

rs140336145

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:209629770 (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>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.000007 (1/140122, GnomAD)
T=0.00003 (1/35432, ALFA)
A=0.00018 (5/28256, 14KJPN) (+ 3 more)
A=0.00024 (4/16760, 8.3KJPN)
A=0.0002 (1/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LAMB3 : 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	35432	G=0.99997	A=0.00000, T=0.00003
European	Sub	26588	G=0.99996	A=0.00000, T=0.00004
African	Sub	2918	G=1.0000	A=0.0000, T=0.0000
African Others	Sub	114	G=1.000	A=0.000, T=0.000
African American	Sub	2804	G=1.0000	A=0.0000, T=0.0000
Asian	Sub	112	G=1.000	A=0.000, T=0.000
East Asian	Sub	86	G=1.00	A=0.00, T=0.00
Other Asian	Sub	26	G=1.00	A=0.00, T=0.00
Latin American 1	Sub	500	G=1.000	A=0.000, T=0.000
Latin American 2	Sub	628	G=1.000	A=0.000, T=0.000
South Asian	Sub	98	G=1.00	A=0.00, T=0.00
Other	Sub	4588	G=1.0000	A=0.0000, T=0.0000

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	140122	G=0.999993	A=0.000007
gnomAD - Genomes	European	Sub	75928	G=1.00000	A=0.00000
gnomAD - Genomes	African	Sub	41930	G=1.00000	A=0.00000
gnomAD - Genomes	American	Sub	13658	G=1.00000	A=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=1.0000	A=0.0000
gnomAD - Genomes	East Asian	Sub	3134	G=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2150	G=0.9995	A=0.0005
Allele Frequency Aggregator	Total	Global	35432	G=0.99997	A=0.00000, T=0.00003
Allele Frequency Aggregator	European	Sub	26588	G=0.99996	A=0.00000, T=0.00004
Allele Frequency Aggregator	Other	Sub	4588	G=1.0000	A=0.0000, T=0.0000
Allele Frequency Aggregator	African	Sub	2918	G=1.0000	A=0.0000, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	628	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	500	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00, T=0.00
14KJPN	JAPANESE	Study-wide	28256	G=0.99982	A=0.00018
8.3KJPN	JAPANESE	Study-wide	16760	G=0.99976	A=0.00024
1000Genomes_30x	Global	Study-wide	6404	G=0.9998	A=0.0002
1000Genomes_30x	African	Sub	1786	G=1.0000	A=0.0000
1000Genomes_30x	Europe	Sub	1266	G=1.0000	A=0.0000
1000Genomes_30x	South Asian	Sub	1202	G=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	G=0.9991	A=0.0009
1000Genomes_30x	American	Sub	980	G=1.000	A=0.000
1000Genomes	Global	Study-wide	5008	G=0.9998	A=0.0002
1000Genomes	African	Sub	1322	G=1.0000	A=0.0000
1000Genomes	East Asian	Sub	1008	G=0.9990	A=0.0010
1000Genomes	Europe	Sub	1006	G=1.0000	A=0.0000
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
1000Genomes	American	Sub	694	G=1.000	A=0.000

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 1	NC_000001.11:g.209629770G>A
GRCh38.p14 chr 1	NC_000001.11:g.209629770G>T
GRCh37.p13 chr 1	NC_000001.10:g.209803115G>A
GRCh37.p13 chr 1	NC_000001.10:g.209803115G>T
LAMB3 RefSeqGene	NG_007116.1:g.27706C>T
LAMB3 RefSeqGene	NG_007116.1:g.27706C>A

Gene: LAMB3, laminin subunit beta 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LAMB3 transcript variant 3	NM_001127641.1:c.1099C>T	R [CGC] > C [TGC]	Coding Sequence Variant
laminin subunit beta-3 precursor	NP_001121113.1:p.Arg367Cys	R (Arg) > C (Cys)	Missense Variant
LAMB3 transcript variant 3	NM_001127641.1:c.1099C>A	R [CGC] > S [AGC]	Coding Sequence Variant
laminin subunit beta-3 precursor	NP_001121113.1:p.Arg367Ser	R (Arg) > S (Ser)	Missense Variant
LAMB3 transcript variant 1	NM_000228.3:c.1099C>T	R [CGC] > C [TGC]	Coding Sequence Variant
laminin subunit beta-3 precursor	NP_000219.2:p.Arg367Cys	R (Arg) > C (Cys)	Missense Variant
LAMB3 transcript variant 1	NM_000228.3:c.1099C>A	R [CGC] > S [AGC]	Coding Sequence Variant
laminin subunit beta-3 precursor	NP_000219.2:p.Arg367Ser	R (Arg) > S (Ser)	Missense Variant
LAMB3 transcript variant 2	NM_001017402.2:c.1099C>T	R [CGC] > C [TGC]	Coding Sequence Variant
laminin subunit beta-3 precursor	NP_001017402.1:p.Arg367Cys	R (Arg) > C (Cys)	Missense Variant
LAMB3 transcript variant 2	NM_001017402.2:c.1099C>A	R [CGC] > S [AGC]	Coding Sequence Variant
laminin subunit beta-3 precursor	NP_001017402.1:p.Arg367Ser	R (Arg) > S (Ser)	Missense Variant
LAMB3 transcript variant X1	XM_005273124.5:c.1099C>T	R [CGC] > C [TGC]	Coding Sequence Variant
laminin subunit beta-3 isoform X1	XP_005273181.1:p.Arg367Cys	R (Arg) > C (Cys)	Missense Variant
LAMB3 transcript variant X1	XM_005273124.5:c.1099C>A	R [CGC] > S [AGC]	Coding Sequence Variant
laminin subunit beta-3 isoform X1	XP_005273181.1:p.Arg367Ser	R (Arg) > S (Ser)	Missense Variant
LAMB3 transcript variant X2	XM_017001272.3:c.907C>T	R [CGC] > C [TGC]	Coding Sequence Variant
laminin subunit beta-3 isoform X2	XP_016856761.1:p.Arg303Cys	R (Arg) > C (Cys)	Missense Variant
LAMB3 transcript variant X2	XM_017001272.3:c.907C>A	R [CGC] > S [AGC]	Coding Sequence Variant
laminin subunit beta-3 isoform X2	XP_016856761.1:p.Arg303Ser	R (Arg) > S (Ser)	Missense Variant
LAMB3 transcript variant X3	XM_047420351.1:c.907C>T	R [CGC] > C [TGC]	Coding Sequence Variant
laminin subunit beta-3 isoform X2	XP_047276307.1:p.Arg303Cys	R (Arg) > C (Cys)	Missense Variant
LAMB3 transcript variant X3	XM_047420351.1:c.907C>A	R [CGC] > S [AGC]	Coding Sequence Variant
laminin subunit beta-3 isoform X2	XP_047276307.1:p.Arg303Ser	R (Arg) > S (Ser)	Missense 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=	A	T
GRCh38.p14 chr 1	NC_000001.11:g.209629770=	NC_000001.11:g.209629770G>A	NC_000001.11:g.209629770G>T
GRCh37.p13 chr 1	NC_000001.10:g.209803115=	NC_000001.10:g.209803115G>A	NC_000001.10:g.209803115G>T
LAMB3 RefSeqGene	NG_007116.1:g.27706=	NG_007116.1:g.27706C>T	NG_007116.1:g.27706C>A
LAMB3 transcript variant 1	NM_000228.3:c.1099=	NM_000228.3:c.1099C>T	NM_000228.3:c.1099C>A
LAMB3 transcript variant 1	NM_000228.2:c.1099=	NM_000228.2:c.1099C>T	NM_000228.2:c.1099C>A
LAMB3 transcript variant 2	NM_001017402.2:c.1099=	NM_001017402.2:c.1099C>T	NM_001017402.2:c.1099C>A
LAMB3 transcript variant 2	NM_001017402.1:c.1099=	NM_001017402.1:c.1099C>T	NM_001017402.1:c.1099C>A
LAMB3 transcript variant 3	NM_001127641.1:c.1099=	NM_001127641.1:c.1099C>T	NM_001127641.1:c.1099C>A
LAMB3 transcript variant X1	XM_005273124.5:c.1099=	XM_005273124.5:c.1099C>T	XM_005273124.5:c.1099C>A
LAMB3 transcript variant X1	XM_005273124.4:c.1099=	XM_005273124.4:c.1099C>T	XM_005273124.4:c.1099C>A
LAMB3 transcript variant X1	XM_005273124.3:c.1099=	XM_005273124.3:c.1099C>T	XM_005273124.3:c.1099C>A
LAMB3 transcript variant X1	XM_005273124.2:c.1099=	XM_005273124.2:c.1099C>T	XM_005273124.2:c.1099C>A
LAMB3 transcript variant X1	XM_005273124.1:c.1099=	XM_005273124.1:c.1099C>T	XM_005273124.1:c.1099C>A
LAMB3 transcript variant X2	XM_017001272.3:c.907=	XM_017001272.3:c.907C>T	XM_017001272.3:c.907C>A
LAMB3 transcript variant X2	XM_017001272.2:c.907=	XM_017001272.2:c.907C>T	XM_017001272.2:c.907C>A
LAMB3 transcript variant X2	XM_017001272.1:c.907=	XM_017001272.1:c.907C>T	XM_017001272.1:c.907C>A
LAMB3 transcript variant X3	XM_047420351.1:c.907=	XM_047420351.1:c.907C>T	XM_047420351.1:c.907C>A
laminin subunit beta-3 precursor	NP_000219.2:p.Arg367=	NP_000219.2:p.Arg367Cys	NP_000219.2:p.Arg367Ser
laminin subunit beta-3 precursor	NP_001017402.1:p.Arg367=	NP_001017402.1:p.Arg367Cys	NP_001017402.1:p.Arg367Ser
laminin subunit beta-3 precursor	NP_001121113.1:p.Arg367=	NP_001121113.1:p.Arg367Cys	NP_001121113.1:p.Arg367Ser
laminin subunit beta-3 isoform X1	XP_005273181.1:p.Arg367=	XP_005273181.1:p.Arg367Cys	XP_005273181.1:p.Arg367Ser
laminin subunit beta-3 isoform X2	XP_016856761.1:p.Arg303=	XP_016856761.1:p.Arg303Cys	XP_016856761.1:p.Arg303Ser
laminin subunit beta-3 isoform X2	XP_047276307.1:p.Arg303=	XP_047276307.1:p.Arg303Cys	XP_047276307.1:p.Arg303Ser

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#.

16 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss329191084	May 09, 2011 (134)
2	1000GENOMES	ss489790106	May 04, 2012 (137)
3	1000GENOMES	ss1294450537	Aug 21, 2014 (142)
4	EVA_EXAC	ss1686038343	Apr 01, 2015 (144)
5	EVA_EXAC	ss1686038344	Apr 01, 2015 (144)
6	GNOMAD	ss2732249267	Nov 08, 2017 (151)
7	EVA	ss3747273447	Jul 12, 2019 (153)
8	GNOMAD	ss4010441461	Apr 25, 2021 (155)
9	TOPMED	ss4481823598	Apr 25, 2021 (155)
10	TOPMED	ss4481823599	Apr 25, 2021 (155)
11	TOMMO_GENOMICS	ss5148208813	Apr 25, 2021 (155)
12	EVA	ss5324475718	Oct 12, 2022 (156)
13	1000G_HIGH_COVERAGE	ss5519632387	Oct 12, 2022 (156)
14	SANFORD_IMAGENETICS	ss5627349089	Oct 12, 2022 (156)
15	TOMMO_GENOMICS	ss5675905360	Oct 12, 2022 (156)
16	EVA	ss5911773206	Oct 12, 2022 (156)
17	1000Genomes	NC_000001.10 - 209803115	Oct 11, 2018 (152)
18	1000Genomes_30x	NC_000001.11 - 209629770	Oct 12, 2022 (156)
19	ExAC Submission ignored due to conflicting rows: Row 5273385 (NC_000001.10:209803114:G:G 121365/121366, NC_000001.10:209803114:G:T 1/121366) Row 5273386 (NC_000001.10:209803114:G:G 121365/121366, NC_000001.10:209803114:G:A 1/121366)	-	Oct 11, 2018 (152)
20	ExAC Submission ignored due to conflicting rows: Row 5273385 (NC_000001.10:209803114:G:G 121365/121366, NC_000001.10:209803114:G:T 1/121366) Row 5273386 (NC_000001.10:209803114:G:G 121365/121366, NC_000001.10:209803114:G:A 1/121366)	-	Oct 11, 2018 (152)
21	gnomAD - Genomes	NC_000001.11 - 209629770	Apr 25, 2021 (155)
22	gnomAD - Exomes Submission ignored due to conflicting rows: Row 1283759 (NC_000001.10:209803114:G:G 251454/251456, NC_000001.10:209803114:G:A 2/251456) Row 1283760 (NC_000001.10:209803114:G:G 251455/251456, NC_000001.10:209803114:G:T 1/251456)	-	Jul 12, 2019 (153)
23	gnomAD - Exomes Submission ignored due to conflicting rows: Row 1283759 (NC_000001.10:209803114:G:G 251454/251456, NC_000001.10:209803114:G:A 2/251456) Row 1283760 (NC_000001.10:209803114:G:G 251455/251456, NC_000001.10:209803114:G:T 1/251456)	-	Jul 12, 2019 (153)
24	8.3KJPN	NC_000001.10 - 209803115	Apr 25, 2021 (155)
25	14KJPN	NC_000001.11 - 209629770	Oct 12, 2022 (156)
26	TopMed Submission ignored due to conflicting rows: Row 45429933 (NC_000001.11:209629769:G:A 1/264690) Row 45429934 (NC_000001.11:209629769:G:T 2/264690)	-	Apr 25, 2021 (155)
27	TopMed Submission ignored due to conflicting rows: Row 45429933 (NC_000001.11:209629769:G:A 1/264690) Row 45429934 (NC_000001.11:209629769:G:T 2/264690)	-	Apr 25, 2021 (155)
28	ALFA	NC_000001.11 - 209629770	Apr 25, 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
5297643, 6178120, ss329191084, ss489790106, ss1294450537, ss1686038344, ss2732249267, ss3747273447, ss5148208813, ss5324475718, ss5627349089	NC_000001.10:209803114:G:A	NC_000001.11:209629769:G:A	(self)
7158322, 38142258, 9742464, 117033, ss4010441461, ss4481823598, ss5519632387, ss5675905360, ss5911773206	NC_000001.11:209629769:G:A	NC_000001.11:209629769:G:A	(self)
ss1686038343, ss2732249267	NC_000001.10:209803114:G:T	NC_000001.11:209629769:G:T	(self)
117033, ss4481823599	NC_000001.11:209629769:G:T	NC_000001.11:209629769: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 rs140336145

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

rs140336145