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dbSNP Short Genetic Variations

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.

rs1421302943

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:112253828-112253832 (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
dupTAGC
Variation Type
Indel Insertion and Deletion
Frequency
dupTAGC=0.000019 (5/264690, TOPMED)
dupTAGC=0.000008 (2/250054, GnomAD_exome)
dupTAGC=0.000029 (4/140300, GnomAD) (+ 1 more)
dupTAGC=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LAMA4 : Stop Gained
LAMA4-AS1 : 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 Alt HMOZ HTRZ HWEP
Total Global 14050 CTAGC=1.00000 CTAGCTAGC=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 CTAGC=1.0000 CTAGCTAGC=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 CTAGC=1.0000 CTAGCTAGC=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 CTAGC=1.000 CTAGCTAGC=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 CTAGC=1.0000 CTAGCTAGC=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 CTAGC=1.000 CTAGCTAGC=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 CTAGC=1.00 CTAGCTAGC=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 CTAGC=1.00 CTAGCTAGC=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CTAGC=1.000 CTAGCTAGC=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 CTAGC=1.000 CTAGCTAGC=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 CTAGC=1.00 CTAGCTAGC=0.00 1.0 0.0 0.0 N/A
Other Sub 496 CTAGC=1.000 CTAGCTAGC=0.000 1.0 0.0 0.0 N/A


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 -

No frequency provided

dupTAGC=0.000019
gnomAD - Exomes Global Study-wide 250054 -

No frequency provided

dupTAGC=0.000008
gnomAD - Exomes European Sub 134990 -

No frequency provided

dupTAGC=0.000000
gnomAD - Exomes Asian Sub 48844 -

No frequency provided

dupTAGC=0.00000
gnomAD - Exomes American Sub 34570 -

No frequency provided

dupTAGC=0.00000
gnomAD - Exomes African Sub 15510 -

No frequency provided

dupTAGC=0.00013
gnomAD - Exomes Ashkenazi Jewish Sub 10068 -

No frequency provided

dupTAGC=0.00000
gnomAD - Exomes Other Sub 6072 -

No frequency provided

dupTAGC=0.0000
gnomAD - Genomes Global Study-wide 140300 -

No frequency provided

dupTAGC=0.000029
gnomAD - Genomes European Sub 75962 -

No frequency provided

dupTAGC=0.00000
gnomAD - Genomes African Sub 42064 -

No frequency provided

dupTAGC=0.00007
gnomAD - Genomes American Sub 13666 -

No frequency provided

dupTAGC=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 -

No frequency provided

dupTAGC=0.0000
gnomAD - Genomes East Asian Sub 3132 -

No frequency provided

dupTAGC=0.0000
gnomAD - Genomes Other Sub 2154 -

No frequency provided

dupTAGC=0.0005
Allele Frequency Aggregator Total Global 14050 CTAGC=1.00000 dupTAGC=0.00000
Allele Frequency Aggregator European Sub 9690 CTAGC=1.0000 dupTAGC=0.0000
Allele Frequency Aggregator African Sub 2898 CTAGC=1.0000 dupTAGC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 CTAGC=1.000 dupTAGC=0.000
Allele Frequency Aggregator Other Sub 496 CTAGC=1.000 dupTAGC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 CTAGC=1.000 dupTAGC=0.000
Allele Frequency Aggregator Asian Sub 112 CTAGC=1.000 dupTAGC=0.000
Allele Frequency Aggregator South Asian Sub 98 CTAGC=1.00 dupTAGC=0.00
Help

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 6 NC_000006.12:g.112253829_112253832dup
GRCh37.p13 chr 6 NC_000006.11:g.112575031_112575034dup
LAMA4 RefSeqGene (LRG_433) NG_008209.1:g.5796_5799dup
GRCh37.p13 chr 6 fix patch HG1304_PATCH NW_003871062.1:g.251350_251353dup
Gene: LAMA4, laminin subunit alpha 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LAMA4 transcript variant 1 NM_001105206.3:c.195+125_…

NM_001105206.3:c.195+125_195+128dup

N/A Intron Variant
LAMA4 transcript variant 3 NM_001105207.3:c.195+125_…

NM_001105207.3:c.195+125_195+128dup

N/A Intron Variant
LAMA4 transcript variant 2 NM_002290.5:c.195+125_195…

NM_002290.5:c.195+125_195+128dup

N/A Intron Variant
LAMA4 transcript variant 4 NM_001105208.3:c.320_323d…

NM_001105208.3:c.320_323dup

R [AGG] > S* [AGCTAGG] Coding Sequence Variant
laminin subunit alpha-4 isoform 3 precursor NP_001098678.1:p.Arg108de…

NP_001098678.1:p.Arg108delinsSerTer

R (Arg) > S* (SerTer) Stop Gained
LAMA4 transcript variant 5 NM_001105209.3:c.320_323d…

NM_001105209.3:c.320_323dup

R [AGG] > S* [AGCTAGG] Coding Sequence Variant
laminin subunit alpha-4 isoform 3 precursor NP_001098679.1:p.Arg108de…

NP_001098679.1:p.Arg108delinsSerTer

R (Arg) > S* (SerTer) Stop Gained
LAMA4 transcript variant X1 XM_005266983.5:c.195+125_…

XM_005266983.5:c.195+125_195+128dup

N/A Intron Variant
LAMA4 transcript variant X2 XM_005266984.5:c.195+125_…

XM_005266984.5:c.195+125_195+128dup

N/A Intron Variant
LAMA4 transcript variant X4 XM_017010854.3:c.195+125_…

XM_017010854.3:c.195+125_195+128dup

N/A Intron Variant
LAMA4 transcript variant X3 XM_047418769.1:c.195+125_…

XM_047418769.1:c.195+125_195+128dup

N/A Intron Variant
LAMA4 transcript variant X5 XM_047418770.1:c.195+125_…

XM_047418770.1:c.195+125_195+128dup

N/A Intron Variant
LAMA4 transcript variant X6 XM_047418771.1:c.195+125_…

XM_047418771.1:c.195+125_195+128dup

N/A Intron Variant
Gene: LAMA4-AS1, LAMA4 antisense RNA 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LAMA4-AS1 transcript NR_121193.1:n. N/A Intron Variant
Help

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
Help

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 CTAGC= dupTAGC
GRCh38.p14 chr 6 NC_000006.12:g.112253828_112253832= NC_000006.12:g.112253829_112253832dup
GRCh37.p13 chr 6 NC_000006.11:g.112575030_112575034= NC_000006.11:g.112575031_112575034dup
LAMA4 RefSeqGene (LRG_433) NG_008209.1:g.5795_5799= NG_008209.1:g.5796_5799dup
LAMA4 transcript variant 5 NM_001105209.3:c.319_323= NM_001105209.3:c.320_323dup
LAMA4 transcript variant 5 NM_001105209.2:c.319_323= NM_001105209.2:c.320_323dup
LAMA4 transcript variant 4 NM_001105208.3:c.319_323= NM_001105208.3:c.320_323dup
LAMA4 transcript variant 4 NM_001105208.2:c.319_323= NM_001105208.2:c.320_323dup
GRCh37.p13 chr 6 fix patch HG1304_PATCH NW_003871062.1:g.251349_251353= NW_003871062.1:g.251350_251353dup
laminin subunit alpha-4 isoform 3 precursor NP_001098679.1:p.Ala107_Arg108= NP_001098679.1:p.Arg108delinsSerTer
laminin subunit alpha-4 isoform 3 precursor NP_001098678.1:p.Ala107_Arg108= NP_001098678.1:p.Arg108delinsSerTer
LAMA4 transcript variant 1 NM_001105206.2:c.195+128= NM_001105206.2:c.195+125_195+128dup
LAMA4 transcript variant 1 NM_001105206.3:c.195+128= NM_001105206.3:c.195+125_195+128dup
LAMA4 transcript variant 3 NM_001105207.2:c.195+128= NM_001105207.2:c.195+125_195+128dup
LAMA4 transcript variant 3 NM_001105207.3:c.195+128= NM_001105207.3:c.195+125_195+128dup
LAMA4 transcript variant 2 NM_002290.4:c.195+128= NM_002290.4:c.195+125_195+128dup
LAMA4 transcript variant 2 NM_002290.5:c.195+128= NM_002290.5:c.195+125_195+128dup
LAMA4 transcript variant X1 XM_005266983.1:c.195+128= XM_005266983.1:c.195+125_195+128dup
LAMA4 transcript variant X1 XM_005266983.5:c.195+128= XM_005266983.5:c.195+125_195+128dup
LAMA4 transcript variant X2 XM_005266984.1:c.195+128= XM_005266984.1:c.195+125_195+128dup
LAMA4 transcript variant X2 XM_005266984.5:c.195+128= XM_005266984.5:c.195+125_195+128dup
LAMA4 transcript variant X1 XM_005277549.1:c.195+128= XM_005277549.1:c.195+125_195+128dup
LAMA4 transcript variant X2 XM_005277550.1:c.195+128= XM_005277550.1:c.195+125_195+128dup
LAMA4 transcript variant X4 XM_017010854.3:c.195+128= XM_017010854.3:c.195+125_195+128dup
LAMA4 transcript variant X3 XM_047418769.1:c.195+128= XM_047418769.1:c.195+125_195+128dup
LAMA4 transcript variant X5 XM_047418770.1:c.195+128= XM_047418770.1:c.195+125_195+128dup
LAMA4 transcript variant X6 XM_047418771.1:c.195+128= XM_047418771.1:c.195+125_195+128dup
Help

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 GNOMAD ss2736015099 Oct 12, 2018 (152)
2 GNOMAD ss4149368780 Apr 26, 2021 (155)
3 TOPMED ss4717782083 Apr 26, 2021 (155)
4 gnomAD - Genomes NC_000006.12 - 112253828 Apr 26, 2021 (155)
5 gnomAD - Exomes NC_000006.11 - 112575030 Jul 13, 2019 (153)
6 TopMed NC_000006.12 - 112253828 Apr 26, 2021 (155)
7 ALFA NC_000006.12 - 112253828 Apr 26, 2021 (155)
Help

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
5164832, ss2736015099 NC_000006.11:112575029::CTAG NC_000006.12:112253827:CTAGC:CTAGC…

NC_000006.12:112253827:CTAGC:CTAGCTAGC

(self)
237700046, 555159641, ss4149368780, ss4717782083 NC_000006.12:112253827::CTAG NC_000006.12:112253827:CTAGC:CTAGC…

NC_000006.12:112253827:CTAGC:CTAGCTAGC

(self)
13229931372 NC_000006.12:112253827:CTAGC:CTAGC…

NC_000006.12:112253827:CTAGC:CTAGCTAGC

NC_000006.12:112253827:CTAGC:CTAGC…

NC_000006.12:112253827:CTAGC:CTAGCTAGC

(self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1421302943

Help

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.

Software version is: 2.0.1.post820+afb47a3d