SNP Links for Gene (Select 2735) - SNP

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Select item 14910721521.

rs1491072152 has merged into rs763366124 [Homo sapiens]

Variant type:: DELINS
Alleles:: TT>- [Show Flanks]
Chromosome:: 12:57459161 (GRCh38)
12:57852944 (GRCh37)
Canonical SPDI:: NC_000012.12:57459158:TTTT:TT
Gene:: GLI1 (Varview), LOC124902947 (Varview)
Functional Consequence:: non_coding_transcript_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by cluster
MAF:: -=0.000007/1 (GnomAD)
HGVS:: NC_000012.12:g.57459161_57459162del, NC_000012.11:g.57852944_57852945del, NG_029564.1:g.4027_4028del, XR_007063335.1:n.632_633del

Select item 14909095992.

rs1490909599 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 12:57461258 (GRCh38)
12:57855041 (GRCh37)
Canonical SPDI:: NC_000012.12:57461257:G:T
Gene:: GLI1 (Varview), LOC124902947 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000012.12:g.57461258G>T, NC_000012.11:g.57855041G>T, NG_029564.1:g.6124G>T

Select item 14908170643.

rs1490817064 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C,G [Show Flanks]
Chromosome:: 12:57461993 (GRCh38)
12:57855776 (GRCh37)
Canonical SPDI:: NC_000012.12:57461992:T:C,NC_000012.12:57461992:T:G
Gene:: GLI1 (Varview), LOC124902947 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
HGVS:: NC_000012.12:g.57461993T>C, NC_000012.12:g.57461993T>G, NC_000012.11:g.57855776T>C, NC_000012.11:g.57855776T>G, NG_029564.1:g.6859T>C, NG_029564.1:g.6859T>G

Select item 14906260224.

rs1490626022 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 12:57461745 (GRCh38)
12:57855528 (GRCh37)
Canonical SPDI:: NC_000012.12:57461744:G:A
Gene:: GLI1 (Varview), LOC124902947 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
A=0.000007/1 (GnomAD)
HGVS:: NC_000012.12:g.57461745G>A, NC_000012.11:g.57855528G>A, NG_029564.1:g.6611G>A

Select item 14904292785.

rs1490429278 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 12:57468746 (GRCh38)
12:57862529 (GRCh37)
Canonical SPDI:: NC_000012.12:57468745:T:C
Gene:: GLI1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
C=0.000014/2 (GnomAD)
HGVS:: NC_000012.12:g.57468746T>C, NC_000012.11:g.57862529T>C, NG_029564.1:g.13612T>C

Select item 14901040746.

rs1490104074 [Homo sapiens]

Variant type:: SNV:
Alleles:: GA>-
Chromosome:: no mapping
Canonical SPDI:

Select item 14900325027.

rs1490032502 [Homo sapiens]

Variant type:: SNV:
Alleles:: A>T
Chromosome:: no mapping
Canonical SPDI:

Select item 14898181728.

rs1489818172 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 12:57461369 (GRCh38)
12:57855152 (GRCh37)
Canonical SPDI:: NC_000012.12:57461368:G:A
Gene:: GLI1 (Varview), LOC124902947 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000012.12:g.57461369G>A, NC_000012.11:g.57855152G>A, NG_029564.1:g.6235G>A

Select item 14893625559.

rs1489362555 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 12:57471332 (GRCh38)
12:57865115 (GRCh37)
Canonical SPDI:: NC_000012.12:57471331:C:T
Gene:: GLI1 (Varview)
Functional Consequence:: coding_sequence_variant,synonymous_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
T=0.000007/1 (GnomAD)
HGVS:: NC_000012.12:g.57471332C>T, NC_000012.11:g.57865115C>T, NG_023205.2:g.22483G>A, NG_029564.1:g.16198C>T, NM_005269.3:c.2592C>T, NM_005269.2:c.2592C>T, NM_001167609.2:c.2469C>T, NM_001167609.1:c.2469C>T, NM_001160045.2:c.2208C>T, NM_001160045.1:c.2208C>T, XM_011538189.3:c.2592C>T, XM_011538189.2:c.2592C>T, XM_011538189.1:c.2592C>T, XM_011538190.3:c.2361C>T, XM_011538190.2:c.2361C>T, XM_011538190.1:c.2361C>T

Select item 148909372810.

rs1489093728 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 12:57462436 (GRCh38)
12:57856219 (GRCh37)
Canonical SPDI:: NC_000012.12:57462435:C:T
Gene:: GLI1 (Varview), LOC124902947 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000012.12:g.57462436C>T, NC_000012.11:g.57856219C>T, NG_029564.1:g.7302C>T

Select item 148907273011.

rs1489072730 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->C [Show Flanks]
Chromosome:: 12:57471905 (GRCh38)
12:57865689 (GRCh37)
Canonical SPDI:: NC_000012.12:57471905:CCCC:CCCCC
Gene:: GLI1 (Varview), ARHGAP9 (Varview)
Functional Consequence:: frameshift_variant,downstream_transcript_variant,coding_sequence_variant,500B_downstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CCCCC=0.000043/1 (ALFA)
C=0.000004/1 (GnomAD_exomes)
C=0.000156/1 (1000Genomes)
HGVS:: NC_000012.12:g.57471909dup, NC_000012.11:g.57865692dup, NG_023205.2:g.21909dup, NG_029564.1:g.16775dup, NM_005269.3:c.3169dup, NM_005269.2:c.3169dup, NM_001167609.2:c.3046dup, NM_001167609.1:c.3046dup, NM_001160045.2:c.2785dup, NM_001160045.1:c.2785dup, XM_011538189.3:c.3169dup, XM_011538189.2:c.3169dup, XM_011538189.1:c.3169dup, XM_011538190.3:c.2938dup, XM_011538190.2:c.2938dup, XM_011538190.1:c.2938dup, NP_005260.1:p.Gln1057fs, NP_001161081.1:p.Gln1016fs, NP_001153517.1:p.Gln929fs, XP_011536491.1:p.Gln1057fs, XP_011536492.1:p.Gln980fs

Select item 148884979912.

rs1488849799 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 12:57472053 (GRCh38)
12:57865836 (GRCh37)
Canonical SPDI:: NC_000012.12:57472052:A:G
Gene:: GLI1 (Varview), ARHGAP9 (Varview)
Functional Consequence:: downstream_transcript_variant,coding_sequence_variant,500B_downstream_variant,missense_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000008/2 (TOPMED)
HGVS:: NC_000012.12:g.57472053A>G, NC_000012.11:g.57865836A>G, NG_023205.2:g.21762T>C, NG_029564.1:g.16919A>G, NM_005269.3:c.3313A>G, NM_005269.2:c.3313A>G, NM_001167609.2:c.3190A>G, NM_001167609.1:c.3190A>G, NM_001160045.2:c.2929A>G, NM_001160045.1:c.2929A>G, XM_011538189.3:c.3313A>G, XM_011538189.2:c.3313A>G, XM_011538189.1:c.3313A>G, XM_011538190.3:c.3082A>G, XM_011538190.2:c.3082A>G, XM_011538190.1:c.3082A>G, NP_005260.1:p.Ser1105Gly, NP_001161081.1:p.Ser1064Gly, NP_001153517.1:p.Ser977Gly, XP_011536491.1:p.Ser1105Gly, XP_011536492.1:p.Ser1028Gly

Select item 148880501213.

rs1488805012 [Homo sapiens]

Variant type:: DELINS
Alleles:: A>- [Show Flanks]
Chromosome:: 12:57467565 (GRCh38)
12:57861348 (GRCh37)
Canonical SPDI:: NC_000012.12:57467564:AAA:AA
Gene:: GLI1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AA=0./0 (ALFA)
-=0.000004/1 (TOPMED)
-=0.000014/2 (GnomAD)
HGVS:: NC_000012.12:g.57467567del, NC_000012.11:g.57861350del, NG_029564.1:g.12433del

Select item 148869373914.

rs1488693739 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 12:57466641 (GRCh38)
12:57860424 (GRCh37)
Canonical SPDI:: NC_000012.12:57466640:C:T
Gene:: GLI1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000008/2 (TOPMED)
T=0.000014/2 (GnomAD)
HGVS:: NC_000012.12:g.57466641C>T, NC_000012.11:g.57860424C>T, NG_029564.1:g.11507C>T

Select item 148832554215.

rs1488325542 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->C [Show Flanks]
Chromosome:: 12:57471977 (GRCh38)
12:57865761 (GRCh37)
Canonical SPDI:: NC_000012.12:57471977:CCCCCC:CCCCCCC
Gene:: GLI1 (Varview), ARHGAP9 (Varview)
Functional Consequence:: frameshift_variant,downstream_transcript_variant,coding_sequence_variant,500B_downstream_variant
Validated:: by frequency,by alfa
MAF:: CCCCCCC=0./0 (ALFA)
HGVS:: NC_000012.12:g.57471983dup, NC_000012.11:g.57865766dup, NG_023205.2:g.21837dup, NG_029564.1:g.16849dup, NM_005269.3:c.3243dup, NM_005269.2:c.3243dup, NM_001167609.2:c.3120dup, NM_001167609.1:c.3120dup, NM_001160045.2:c.2859dup, NM_001160045.1:c.2859dup, XM_011538189.3:c.3243dup, XM_011538189.2:c.3243dup, XM_011538189.1:c.3243dup, XM_011538190.3:c.3012dup, XM_011538190.2:c.3012dup, XM_011538190.1:c.3012dup, NP_005260.1:p.Asn1082fs, NP_001161081.1:p.Asn1041fs, NP_001153517.1:p.Asn954fs, XP_011536491.1:p.Asn1082fs, XP_011536492.1:p.Asn1005fs

Select item 148824385116.

rs1488243851 [Homo sapiens]

Variant type:: DELINS
Alleles:: CC>- [Show Flanks]
Chromosome:: 12:57462408 (GRCh38)
12:57856191 (GRCh37)
Canonical SPDI:: NC_000012.12:57462406:CCC:C
Gene:: GLI1 (Varview), LOC124902947 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
-=0.000008/2 (TOPMED)
-=0.000014/2 (GnomAD)
HGVS:: NC_000012.12:g.57462408_57462409del, NC_000012.11:g.57856191_57856192del, NG_029564.1:g.7274_7275del

Select item 148807894317.

rs1488078943 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 12:57471492 (GRCh38)
12:57865275 (GRCh37)
Canonical SPDI:: NC_000012.12:57471491:G:T
Gene:: GLI1 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
T=0.000007/1 (GnomAD)
HGVS:: NC_000012.12:g.57471492G>T, NC_000012.11:g.57865275G>T, NG_023205.2:g.22323C>A, NG_029564.1:g.16358G>T, NM_005269.3:c.2752G>T, NM_005269.2:c.2752G>T, NM_001167609.2:c.2629G>T, NM_001167609.1:c.2629G>T, NM_001160045.2:c.2368G>T, NM_001160045.1:c.2368G>T, XM_011538189.3:c.2752G>T, XM_011538189.2:c.2752G>T, XM_011538189.1:c.2752G>T, XM_011538190.3:c.2521G>T, XM_011538190.2:c.2521G>T, XM_011538190.1:c.2521G>T, NP_005260.1:p.Ala918Ser, NP_001161081.1:p.Ala877Ser, NP_001153517.1:p.Ala790Ser, XP_011536491.1:p.Ala918Ser, XP_011536492.1:p.Ala841Ser

Select item 148791789618.

rs1487917896 [Homo sapiens]

Variant type:: DELINS
Alleles:: G>-,GG,GGGGGGG,GGGGGGGG [Show Flanks]
Chromosome:: 12:57460076 (GRCh38)
12:57853859 (GRCh37)
Canonical SPDI:: NC_000012.12:57460075:GGGGGGG:GGGGGG,NC_000012.12:57460075:GGGGGGG:GGGGGGGG,NC_000012.12:57460075:GGGGGGG:GGGGGGGGGGGGG,NC_000012.12:57460075:GGGGGGG:GGGGGGGGGGGGGG
Gene:: GLI1 (Varview), LOC124902947 (Varview)
Functional Consequence:: 5_prime_UTR_variant,intron_variant,genic_upstream_transcript_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GGGGGGGG=0./0 (ALFA)
HGVS:: NC_000012.12:g.57460082del, NC_000012.12:g.57460082dup, NC_000012.12:g.57460077_57460082dup, NC_000012.12:g.57460076_57460082dup, NC_000012.11:g.57853865del, NC_000012.11:g.57853865dup, NC_000012.11:g.57853860_57853865dup, NC_000012.11:g.57853859_57853865dup, NG_029564.1:g.4948del, NG_029564.1:g.4948dup, NG_029564.1:g.4943_4948dup, NG_029564.1:g.4942_4948dup, NM_005269.3:c.-147del, NM_005269.3:c.-147dup, NM_005269.3:c.-152_-147dup, NM_005269.3:c.-153_-147dup, NM_001167609.2:c.-147del, NM_001167609.2:c.-147dup, NM_001167609.2:c.-152_-147dup, NM_001167609.2:c.-153_-147dup, NM_001160045.2:c.-311del, NM_001160045.2:c.-311dup, NM_001160045.2:c.-316_-311dup, NM_001160045.2:c.-317_-311dup, XM_011538190.3:c.-147del, XM_011538190.3:c.-147dup, XM_011538190.3:c.-152_-147dup, XM_011538190.3:c.-153_-147dup

Select item 148782974319.

rs1487829743 [Homo sapiens]

Variant type:: DELINS
Alleles:: C>- [Show Flanks]
Chromosome:: 12:57465595 (GRCh38)
12:57859378 (GRCh37)
Canonical SPDI:: NC_000012.12:57465594:CCCC:CCC
Gene:: GLI1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by cluster
MAF:: -=0.00021/4 (TOMMO)
HGVS:: NC_000012.12:g.57465598del, NC_000012.11:g.57859381del, NG_029564.1:g.10464del

Select item 148769202320.

rs1487692023 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C,T [Show Flanks]
Chromosome:: 12:57469894 (GRCh38)
12:57863677 (GRCh37)
Canonical SPDI:: NC_000012.12:57469893:G:A,NC_000012.12:57469893:G:C,NC_000012.12:57469893:G:T
Gene:: GLI1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
HGVS:: NC_000012.12:g.57469894G>A, NC_000012.12:g.57469894G>C, NC_000012.12:g.57469894G>T, NC_000012.11:g.57863677G>A, NC_000012.11:g.57863677G>C, NC_000012.11:g.57863677G>T, NG_029564.1:g.14760G>A, NG_029564.1:g.14760G>C, NG_029564.1:g.14760G>T

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