SNP Links for Gene (Select 26045) - SNP

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Select item 14915787551.

rs1491578755 has merged into rs34328033 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTTTTTT>-,TTT,TTTT,TTTTT,TTTTTT,TTTTTTTT,TTTTTTTTT,TTTTTTTTTT,TTTTTTTTTTT,TTTTTTTTTTTTT,TTTTTTTTTTTTTTTTTTTT [Show Flanks]
Chromosome:: 5:138869383 (GRCh38)
5:138205072 (GRCh37)
Canonical SPDI:: NC_000005.10:138869374:TTTTTTTTTTTTTTT:TTTTTTTT,NC_000005.10:138869374:TTTTTTTTTTTTTTT:TTTTTTTTTTT,NC_000005.10:138869374:TTTTTTTTTTTTTTT:TTTTTTTTTTTT,NC_000005.10:138869374:TTTTTTTTTTTTTTT:TTTTTTTTTTTTT,NC_000005.10:138869374:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTT,NC_000005.10:138869374:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTT,NC_000005.10:138869374:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT,NC_000005.10:138869374:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTT,NC_000005.10:138869374:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTT,NC_000005.10:138869374:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTT,NC_000005.10:138869374:TTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTTTTTTTT
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: 3_prime_UTR_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTTT=0./0 (ALFA)
-=0.26857/1345 (1000Genomes)
-=0.28859/172 (NorthernSweden)
-=0.2891/1072 (TWINSUK)
-=0.29009/1118 (ALSPAC)
-=0.325/13 (GENOME_DK)
HGVS:: NC_000005.10:g.138869383_138869389del, NC_000005.10:g.138869386_138869389del, NC_000005.10:g.138869387_138869389del, NC_000005.10:g.138869388_138869389del, NC_000005.10:g.138869389del, NC_000005.10:g.138869389dup, NC_000005.10:g.138869388_138869389dup, NC_000005.10:g.138869387_138869389dup, NC_000005.10:g.138869386_138869389dup, NC_000005.10:g.138869384_138869389dup, NC_000005.10:g.138869377_138869389dup, NC_000005.9:g.138205072_138205078del, NC_000005.9:g.138205075_138205078del, NC_000005.9:g.138205076_138205078del, NC_000005.9:g.138205077_138205078del, NC_000005.9:g.138205078del, NC_000005.9:g.138205078dup, NC_000005.9:g.138205077_138205078dup, NC_000005.9:g.138205076_138205078dup, NC_000005.9:g.138205075_138205078dup, NC_000005.9:g.138205073_138205078dup, NC_000005.9:g.138205066_138205078dup, NG_047029.1:g.120988_120994del, NG_047029.1:g.120991_120994del, NG_047029.1:g.120992_120994del, NG_047029.1:g.120993_120994del, NG_047029.1:g.120994del, NG_047029.1:g.120994dup, NG_047029.1:g.120993_120994dup, NG_047029.1:g.120992_120994dup, NG_047029.1:g.120991_120994dup, NG_047029.1:g.120989_120994dup, NG_047029.1:g.120982_120994dup, NM_015564.3:c.*3629_*3635del, NM_015564.3:c.*3632_*3635del, NM_015564.3:c.*3633_*3635del, NM_015564.3:c.*3634_*3635del, NM_015564.3:c.*3635del, NM_015564.3:c.*3635dup, NM_015564.3:c.*3634_*3635dup, NM_015564.3:c.*3633_*3635dup, NM_015564.3:c.*3632_*3635dup, NM_015564.3:c.*3630_*3635dup, NM_015564.3:c.*3623_*3635dup

Select item 14914056832.

rs1491405683 [Homo sapiens]

Variant type:: INS
Alleles:: ->TGTA [Show Flanks]
Chromosome:: 5:138872068 (GRCh38)
5:138207758 (GRCh37)
Canonical SPDI:: NC_000005.10:138872068::TGTA
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TGTA=0./0 (ALFA)
TGTA=0.000004/1 (TOPMED)
TGTA=0.000031/2 (GnomAD)
HGVS:: NC_000005.10:g.138872068_138872069insTGTA, NC_000005.9:g.138207757_138207758insTGTA, NG_047029.1:g.123673_123674insTGTA, NM_015564.3:c.*941_*942insTACA, NM_015564.2:c.*941_*942insTACA

Select item 14912964733.

rs1491296473 [Homo sapiens]

Variant type:: INS
Alleles:: ->C [Show Flanks]
Chromosome:: 5:138869375 (GRCh38)
5:138205065 (GRCh37)
Canonical SPDI:: NC_000005.10:138869375::C
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.0001/7 (GnomAD)
HGVS:: NC_000005.10:g.138869375_138869376insC, NC_000005.9:g.138205064_138205065insC, NG_047029.1:g.120980_120981insC, NM_015564.3:c.*3634_*3635insG

Select item 14911220124.

rs1491122012 [Homo sapiens]

Variant type:: DELINS
Alleles:: GC>-,GCGC,GCGCGC [Show Flanks]
Chromosome:: 5:138872070 (GRCh38)
5:138207759 (GRCh37)
Canonical SPDI:: NC_000005.10:138872067:GCGC:GC,NC_000005.10:138872067:GCGC:GCGCGC,NC_000005.10:138872067:GCGC:GCGCGCGC
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GCGCGC=0./0 (ALFA)
-=0.00365/103 (TOMMO)
HGVS:: NC_000005.10:g.138872068GC[1], NC_000005.10:g.138872068GC[3], NC_000005.10:g.138872068GC[4], NC_000005.9:g.138207757GC[1], NC_000005.9:g.138207757GC[3], NC_000005.9:g.138207757GC[4], NG_047029.1:g.123673GC[1], NG_047029.1:g.123673GC[3], NG_047029.1:g.123673GC[4], NM_015564.3:c.*939GC[1], NM_015564.3:c.*939GC[3], NM_015564.3:c.*939GC[4], NM_015564.2:c.*939GC[1], NM_015564.2:c.*939GC[3], NM_015564.2:c.*939GC[4]

Select item 14910772995.

rs1491077299 has merged into rs35414819 [Homo sapiens]

Variant type:: DELINS
Alleles:: AAAAAAAA>-,AA,AAAAA,AAAAAA,AAAAAAA,AAAAAAAAA,AAAAAAAAAA,AAAAAAAAAAA,AAAAAAAAAAAA,AAAAAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAAAA [Show Flanks]
Chromosome:: 5:138869183 (GRCh38)
5:138204872 (GRCh37)
Canonical SPDI:: NC_000005.10:138869173:AAAAAAAAAAAAAAAAA:AAAAAAAAA,NC_000005.10:138869173:AAAAAAAAAAAAAAAAA:AAAAAAAAAAA,NC_000005.10:138869173:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAA,NC_000005.10:138869173:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA,NC_000005.10:138869173:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA,NC_000005.10:138869173:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA,NC_000005.10:138869173:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAA,NC_000005.10:138869173:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA,NC_000005.10:138869173:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAA,NC_000005.10:138869173:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAAA,NC_000005.10:138869173:AAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAAAA
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: 3_prime_UTR_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAAAAAA=0./0 (ALFA)
-=0.1583/793 (1000Genomes)
AA=0.2896/1074 (TWINSUK)
AA=0.2906/1120 (ALSPAC)
HGVS:: NC_000005.10:g.138869183_138869190del, NC_000005.10:g.138869185_138869190del, NC_000005.10:g.138869188_138869190del, NC_000005.10:g.138869189_138869190del, NC_000005.10:g.138869190del, NC_000005.10:g.138869190dup, NC_000005.10:g.138869189_138869190dup, NC_000005.10:g.138869188_138869190dup, NC_000005.10:g.138869187_138869190dup, NC_000005.10:g.138869181_138869190dup, NC_000005.10:g.138869180_138869190dup, NC_000005.9:g.138204872_138204879del, NC_000005.9:g.138204874_138204879del, NC_000005.9:g.138204877_138204879del, NC_000005.9:g.138204878_138204879del, NC_000005.9:g.138204879del, NC_000005.9:g.138204879dup, NC_000005.9:g.138204878_138204879dup, NC_000005.9:g.138204877_138204879dup, NC_000005.9:g.138204876_138204879dup, NC_000005.9:g.138204870_138204879dup, NC_000005.9:g.138204869_138204879dup, NG_047029.1:g.120788_120795del, NG_047029.1:g.120790_120795del, NG_047029.1:g.120793_120795del, NG_047029.1:g.120794_120795del, NG_047029.1:g.120795del, NG_047029.1:g.120795dup, NG_047029.1:g.120794_120795dup, NG_047029.1:g.120793_120795dup, NG_047029.1:g.120792_120795dup, NG_047029.1:g.120786_120795dup, NG_047029.1:g.120785_120795dup, NM_015564.3:c.*3829_*3836del, NM_015564.3:c.*3831_*3836del, NM_015564.3:c.*3834_*3836del, NM_015564.3:c.*3835_*3836del, NM_015564.3:c.*3836del, NM_015564.3:c.*3836dup, NM_015564.3:c.*3835_*3836dup, NM_015564.3:c.*3834_*3836dup, NM_015564.3:c.*3833_*3836dup, NM_015564.3:c.*3827_*3836dup, NM_015564.3:c.*3826_*3836dup

Select item 14907147476.

rs1490714747 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:138873970 (GRCh38)
5:138209659 (GRCh37)
Canonical SPDI:: NC_000005.10:138873969:A:G
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,synonymous_variant,coding_sequence_variant,genic_upstream_transcript_variant
Validated:: by frequency
MAF:: G=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000005.10:g.138873970A>G, NC_000005.9:g.138209659A>G, NG_047029.1:g.125575A>G, NM_015564.3:c.591T>C, NM_015564.2:c.591T>C

Select item 14905894777.

rs1490589477 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 5:138870817 (GRCh38)
5:138206506 (GRCh37)
Canonical SPDI:: NC_000005.10:138870816:G:A
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
HGVS:: NC_000005.10:g.138870817G>A, NC_000005.9:g.138206506G>A, NG_047029.1:g.122422G>A, NM_015564.3:c.*2193C>T, NM_015564.2:c.*2193C>T

Select item 14904797118.

rs1490479711 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 5:138873385 (GRCh38)
5:138209074 (GRCh37)
Canonical SPDI:: NC_000005.10:138873384:C:T
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,synonymous_variant,coding_sequence_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000005.10:g.138873385C>T, NC_000005.9:g.138209074C>T, NG_047029.1:g.124990C>T, NM_015564.3:c.1176G>A, NM_015564.2:c.1176G>A

Select item 14900600639.

rs1490060063 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G,T [Show Flanks]
Chromosome:: 5:138875753 (GRCh38)
5:138211442 (GRCh37)
Canonical SPDI:: NC_000005.10:138875752:C:G,NC_000005.10:138875752:C:T
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000023/6 (TOPMED)
G=0.000071/1 (TOMMO)
HGVS:: NC_000005.10:g.138875753C>G, NC_000005.10:g.138875753C>T, NC_000005.9:g.138211442C>G, NC_000005.9:g.138211442C>T, NG_047029.1:g.127358C>G, NG_047029.1:g.127358C>T

Select item 148953672410.

rs1489536724 [Homo sapiens]

Variant type:: DELINS
Alleles:: TGAAT>- [Show Flanks]
Chromosome:: 5:138875141 (GRCh38)
5:138210830 (GRCh37)
Canonical SPDI:: NC_000005.10:138875139:TTGAAT:T
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,intron_variant,upstream_transcript_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
HGVS:: NC_000005.10:g.138875141_138875145del, NC_000005.9:g.138210830_138210834del, NG_047029.1:g.126746_126750del, NM_015564.3:c.-233_-229del, NM_015564.2:c.-233_-229del

Select item 148942873211.

rs1489428732 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 5:138872798 (GRCh38)
5:138208487 (GRCh37)
Canonical SPDI:: NC_000005.10:138872797:G:C
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
HGVS:: NC_000005.10:g.138872798G>C, NC_000005.9:g.138208487G>C, NG_047029.1:g.124403G>C, NM_015564.3:c.*212C>G, NM_015564.2:c.*212C>G

Select item 148934585912.

rs1489345859 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 5:138871971 (GRCh38)
5:138207660 (GRCh37)
Canonical SPDI:: NC_000005.10:138871970:T:G
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.000071/1 (ALFA)
G=0.000015/4 (TOPMED)
HGVS:: NC_000005.10:g.138871971T>G, NC_000005.9:g.138207660T>G, NG_047029.1:g.123576T>G, NM_015564.3:c.*1039A>C, NM_015564.2:c.*1039A>C

Select item 148922301113.

rs1489223011 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 5:138871989 (GRCh38)
5:138207678 (GRCh37)
Canonical SPDI:: NC_000005.10:138871988:G:A
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000071/1 (ALFA)
A=0.000026/7 (TOPMED)
A=0.000425/7 (TOMMO)
A=0.001711/5 (KOREAN)
HGVS:: NC_000005.10:g.138871989G>A, NC_000005.9:g.138207678G>A, NG_047029.1:g.123594G>A, NM_015564.3:c.*1021C>T, NM_015564.2:c.*1021C>T

Select item 148868747314.

rs1488687473 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:138873644 (GRCh38)
5:138209333 (GRCh37)
Canonical SPDI:: NC_000005.10:138873643:A:G
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,coding_sequence_variant,genic_upstream_transcript_variant,missense_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.000077/2 (ALFA)
G=0.000007/1 (GnomAD)
G=0.000223/1 (Estonian)
HGVS:: NC_000005.10:g.138873644A>G, NC_000005.9:g.138209333A>G, NG_047029.1:g.125249A>G, NM_015564.3:c.917T>C, NM_015564.2:c.917T>C, NP_056379.1:p.Val306Ala

Select item 148814309115.

rs1488143091 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 5:138874124 (GRCh38)
5:138209813 (GRCh37)
Canonical SPDI:: NC_000005.10:138874123:G:A
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,coding_sequence_variant,genic_upstream_transcript_variant,missense_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000071/1 (ALFA)
A=0.000011/3 (TOPMED)
A=0.000014/2 (GnomAD)
HGVS:: NC_000005.10:g.138874124G>A, NC_000005.9:g.138209813G>A, NG_047029.1:g.125729G>A, NM_015564.3:c.437C>T, NM_015564.2:c.437C>T, NP_056379.1:p.Ser146Leu

Select item 148786183016.

rs1487861830 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 5:138869583 (GRCh38)
5:138205272 (GRCh37)
Canonical SPDI:: NC_000005.10:138869582:G:C
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000026/7 (TOPMED)
C=0.000036/5 (GnomAD)
HGVS:: NC_000005.10:g.138869583G>C, NC_000005.9:g.138205272G>C, NG_047029.1:g.121188G>C, NM_015564.3:c.*3427C>G, NM_015564.2:c.*3427C>G

Select item 148705537017.

rs1487055370 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 5:138874041 (GRCh38)
5:138209730 (GRCh37)
Canonical SPDI:: NC_000005.10:138874040:C:T
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,coding_sequence_variant,genic_upstream_transcript_variant,missense_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000007/1 (GnomAD)
T=0.000008/2 (TOPMED)
HGVS:: NC_000005.10:g.138874041C>T, NC_000005.9:g.138209730C>T, NG_047029.1:g.125646C>T, NM_015564.3:c.520G>A, NM_015564.2:c.520G>A, NP_056379.1:p.Val174Ile

Select item 148702406118.

rs1487024061 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 5:138869193 (GRCh38)
5:138204882 (GRCh37)
Canonical SPDI:: NC_000005.10:138869192:G:A
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000039/5 (GnomAD)
A=0.000672/11 (TOMMO)
A=0.001092/2 (Korea1K)
HGVS:: NC_000005.10:g.138869193G>A, NC_000005.9:g.138204882G>A, NG_047029.1:g.120798G>A, NM_015564.3:c.*3817C>T

Select item 148596177119.

rs1485961771 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 5:138872593 (GRCh38)
5:138208282 (GRCh37)
Canonical SPDI:: NC_000005.10:138872592:C:G
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000011/3 (TOPMED)
G=0.000014/2 (GnomAD)
HGVS:: NC_000005.10:g.138872593C>G, NC_000005.9:g.138208282C>G, NG_047029.1:g.124198C>G, NM_015564.3:c.*417G>C, NM_015564.2:c.*417G>C

Select item 148579443720.

rs1485794437 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 5:138869160 (GRCh38)
5:138204849 (GRCh37)
Canonical SPDI:: NC_000005.10:138869159:C:G
Gene:: CTNNA1 (Varview), LRRTM2 (Varview)
Functional Consequence:: genic_upstream_transcript_variant,3_prime_UTR_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
G=0.000008/1 (GnomAD)
HGVS:: NC_000005.10:g.138869160C>G, NC_000005.9:g.138204849C>G, NG_047029.1:g.120765C>G, NM_015564.3:c.*3850G>C

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