SNP Links for Gene (Select 259173) - SNP

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Select item 14915200061.

rs1491520006 [Homo sapiens]

Variant type:: DELINS
Alleles:: AG>- [Show Flanks]
Chromosome:: 3:46693025 (GRCh38)
3:46734515 (GRCh37)
Canonical SPDI:: NC_000003.12:46693021:GAGAG:GAG
Gene:: ALS2CL (Varview), TMIE (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GAG=0.000071/1 (ALFA)
-=0.000007/1 (GnomAD)
-=0.000019/5 (TOPMED)
HGVS:: NC_000003.12:g.46693023AG[1], NC_000003.11:g.46734513AG[1]

Select item 14914797352.

rs1491479735 has merged into rs1029410954 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTTTT>-,T,TT,TTT,TTTT,TTTTTT,TTTTTTT,TTTTTTTT,TTTTTTTTT,TTTTTTTTTT,TTTTTTTTTTTTTT,TTTTTTTTTTTTTTT [Show Flanks]
Chromosome:: 3:46691736 (GRCh38)
3:46733226 (GRCh37)
Canonical SPDI:: NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTT,NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTT,NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTT,NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTT,NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT,NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTT,NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTT,NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTT,NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTT,NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTTT,NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTTTTTTT,NC_000003.12:46691722:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTTTTTTTT
Gene:: ALS2CL (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTTTTTT=0./0 (ALFA)
-=0.05/2 (GENOME_DK)
HGVS:: NC_000003.12:g.46691736_46691740del, NC_000003.12:g.46691737_46691740del, NC_000003.12:g.46691738_46691740del, NC_000003.12:g.46691739_46691740del, NC_000003.12:g.46691740del, NC_000003.12:g.46691740dup, NC_000003.12:g.46691739_46691740dup, NC_000003.12:g.46691738_46691740dup, NC_000003.12:g.46691737_46691740dup, NC_000003.12:g.46691736_46691740dup, NC_000003.12:g.46691732_46691740dup, NC_000003.12:g.46691731_46691740dup, NC_000003.11:g.46733226_46733230del, NC_000003.11:g.46733227_46733230del, NC_000003.11:g.46733228_46733230del, NC_000003.11:g.46733229_46733230del, NC_000003.11:g.46733230del, NC_000003.11:g.46733230dup, NC_000003.11:g.46733229_46733230dup, NC_000003.11:g.46733228_46733230dup, NC_000003.11:g.46733227_46733230dup, NC_000003.11:g.46733226_46733230dup, NC_000003.11:g.46733222_46733230dup, NC_000003.11:g.46733221_46733230dup

Select item 14913369403.

rs1491336940 [Homo sapiens]

Variant type:: DEL
Alleles:: TG>- [Show Flanks]
Chromosome:: 3:46693706 (GRCh38)
3:46735196 (GRCh37)
Canonical SPDI:: NC_000003.12:46693705:TG:
Gene:: ALS2CL (Varview), TMIE (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency
MAF:: -=0.000145/20 (GnomAD)
HGVS:: NC_000003.12:g.46693706_46693707del, NC_000003.11:g.46735196_46735197del, NG_077216.1:g.328_329del, NM_147129.4:c.-90_-89del, NR_033815.2:n.7_8del, NR_135622.1:n.7_8del

Select item 14912841444.

rs1491284144 [Homo sapiens]

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

Select item 14912515395.

rs1491251539 has merged into rs1377669607 [Homo sapiens]

Variant type:: DELINS
Alleles:: TCCCGCCCCCTGCCAG>-,TCCCGCCCCCTGCCAGTCCCGCCCCCTGCCAG [Show Flanks]
Chromosome:: 3:46693719 (GRCh38)
3:46735209 (GRCh37)
Canonical SPDI:: NC_000003.12:46693706:GCCCCCTGCCAGTCCCGCCCCCTGCCAG:GCCCCCTGCCAG,NC_000003.12:46693706:GCCCCCTGCCAGTCCCGCCCCCTGCCAG:GCCCCCTGCCAGTCCCGCCCCCTGCCAGTCCCGCCCCCTGCCAG
Gene:: ALS2CL (Varview), TMIE (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GCCCCCTGCCAGTCCCGCCCCCTGCCAGTCCCGCCCCCTGCCAG=0./0 (ALFA)
-=0.00004/1 (TOMMO)
-=0.00023/19 (GnomAD)
HGVS:: NC_000003.12:g.46693719_46693734del, NC_000003.12:g.46693719_46693734dup, NC_000003.11:g.46735209_46735224del, NC_000003.11:g.46735209_46735224dup, NG_077216.1:g.341_356del, NG_077216.1:g.341_356dup

Select item 14907811606.

rs1490781160 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:46687569 (GRCh38)
3:46729059 (GRCh37)
Canonical SPDI:: NC_000003.12:46687568:C:T
Gene:: ALS2CL (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000008/2 (TOPMED)
HGVS:: NC_000003.12:g.46687569C>T, NC_000003.11:g.46729059C>T

Select item 14907552287.

rs1490755228 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:46686478 (GRCh38)
3:46727968 (GRCh37)
Canonical SPDI:: NC_000003.12:46686477:C:T
Gene:: ALS2CL (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
T=0.000007/1 (GnomAD)
T=0.000342/1 (KOREAN)
HGVS:: NC_000003.12:g.46686478C>T, NC_000003.11:g.46727968C>T

Select item 14903668888.

rs1490366888 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,T [Show Flanks]
Chromosome:: 3:46679826 (GRCh38)
3:46721316 (GRCh37)
Canonical SPDI:: NC_000003.12:46679825:C:A,NC_000003.12:46679825:C:T
Gene:: ALS2CL (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
HGVS:: NC_000003.12:g.46679826C>A, NC_000003.12:g.46679826C>T, NC_000003.11:g.46721316C>A, NC_000003.11:g.46721316C>T

Select item 14903599899.

rs1490359989 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 3:46694915 (GRCh38)
3:46736405 (GRCh37)
Canonical SPDI:: NC_000003.12:46694914:G:T
Gene:: ALS2CL (Varview), TMIE (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant,genic_upstream_transcript_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_000003.12:g.46694915G>T, NC_000003.11:g.46736405G>T

Select item 149027359810.

rs1490273598 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,G [Show Flanks]
Chromosome:: 3:46685721 (GRCh38)
3:46727211 (GRCh37)
Canonical SPDI:: NC_000003.12:46685720:A:C,NC_000003.12:46685720:A:G
Gene:: ALS2CL (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
G=0.000014/2 (GnomAD)
HGVS:: NC_000003.12:g.46685721A>C, NC_000003.12:g.46685721A>G, NC_000003.11:g.46727211A>C, NC_000003.11:g.46727211A>G

Select item 149026109711.

rs1490261097 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:46687018 (GRCh38)
3:46728508 (GRCh37)
Canonical SPDI:: NC_000003.12:46687017:G:A
Gene:: ALS2CL (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant,non_coding_transcript_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_000003.12:g.46687018G>A, NC_000003.11:g.46728508G>A, NM_147129.5:c.499C>T, NM_147129.4:c.499C>T, NM_147129.3:c.499C>T, NR_033815.3:n.561C>T, NR_033815.2:n.595C>T, NR_033815.1:n.586C>T, NR_135622.2:n.561C>T, NR_135622.1:n.595C>T, NM_001190707.2:c.499C>T, NM_001190707.1:c.499C>T, NM_182774.1:c.499C>T, NP_667340.2:p.Leu167Phe, NP_001177636.1:p.Leu167Phe

Select item 148996845412.

rs1489968454 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: 3:46672441 (GRCh38)
3:46713931 (GRCh37)
Canonical SPDI:: NC_000003.12:46672440:A:T
Gene:: ALS2CL (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000003.12:g.46672441A>T, NC_000003.11:g.46713931A>T

Select item 148993385213.

rs1489933852 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:46687123 (GRCh38)
3:46728613 (GRCh37)
Canonical SPDI:: NC_000003.12:46687122:C:T
Gene:: ALS2CL (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant,non_coding_transcript_variant
Validated:: by frequency
MAF:: T=0.000007/1 (GnomAD_exomes)
HGVS:: NC_000003.12:g.46687123C>T, NC_000003.11:g.46728613C>T, NM_147129.5:c.394G>A, NM_147129.4:c.394G>A, NM_147129.3:c.394G>A, NR_033815.3:n.456G>A, NR_033815.2:n.490G>A, NR_033815.1:n.481G>A, NR_135622.2:n.456G>A, NR_135622.1:n.490G>A, NM_001190707.2:c.394G>A, NM_001190707.1:c.394G>A, NM_182774.1:c.394G>A, NP_667340.2:p.Ala132Thr, NP_001177636.1:p.Ala132Thr

Select item 148984333414.

rs1489843334 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: 3:46689511 (GRCh38)
3:46731001 (GRCh37)
Canonical SPDI:: NC_000003.12:46689510:G:A,NC_000003.12:46689510:G:C
Gene:: ALS2CL (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
HGVS:: NC_000003.12:g.46689511G>A, NC_000003.12:g.46689511G>C, NC_000003.11:g.46731001G>A, NC_000003.11:g.46731001G>C

Select item 148963310115.

rs1489633101 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 3:46684035 (GRCh38)
3:46725525 (GRCh37)
Canonical SPDI:: NC_000003.12:46684034:G:C
Gene:: ALS2CL (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant,non_coding_transcript_variant
Validated:: by frequency
MAF:: C=0.000006/1 (GnomAD_exomes)
HGVS:: NC_000003.12:g.46684035G>C, NC_000003.11:g.46725525G>C, NM_147129.5:c.799C>G, NM_147129.4:c.799C>G, NM_147129.3:c.799C>G, NR_033815.3:n.861C>G, NR_033815.2:n.895C>G, NR_033815.1:n.886C>G, NR_135622.2:n.861C>G, NR_135622.1:n.895C>G, NM_001190707.2:c.799C>G, NM_001190707.1:c.799C>G, NM_182774.1:c.799C>G, NP_667340.2:p.His267Asp, NP_001177636.1:p.His267Asp

Select item 148952033316.

rs1489520333 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:46676264 (GRCh38)
3:46717754 (GRCh37)
Canonical SPDI:: NC_000003.12:46676263:C:T
Gene:: ALS2CL (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant,non_coding_transcript_variant
Validated:: by frequency,by cluster
MAF:: T=0.000004/1 (GnomAD_exomes)
T=0.000007/1 (GnomAD)
HGVS:: NC_000003.12:g.46676264C>T, NC_000003.11:g.46717754C>T, NM_147129.5:c.2167G>A, NM_147129.4:c.2167G>A, NM_147129.3:c.2167G>A, NR_033815.3:n.2225G>A, NR_033815.2:n.2259G>A, NR_033815.1:n.2250G>A, NR_135622.2:n.2225G>A, NR_135622.1:n.2259G>A, NM_001190707.2:c.2167G>A, NM_001190707.1:c.2167G>A, NM_182775.2:c.208G>A, NM_182774.1:c.2167G>A, NP_667340.2:p.Glu723Lys, NP_001177636.1:p.Glu723Lys

Select item 148945026417.

rs1489450264 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:46676487 (GRCh38)
3:46717977 (GRCh37)
Canonical SPDI:: NC_000003.12:46676486:C:T
Gene:: ALS2CL (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000011/3 (TOPMED)
T=0.000021/3 (GnomAD)
HGVS:: NC_000003.12:g.46676487C>T, NC_000003.11:g.46717977C>T

Select item 148923241018.

rs1489232410 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 3:46692864 (GRCh38)
3:46734354 (GRCh37)
Canonical SPDI:: NC_000003.12:46692863:C:G
Gene:: ALS2CL (Varview), TMIE (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.000071/1 (ALFA)
G=0.000021/3 (GnomAD)
G=0.000026/7 (TOPMED)
HGVS:: NC_000003.12:g.46692864C>G, NC_000003.11:g.46734354C>G

Select item 148909963319.

rs1489099633 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:46693887 (GRCh38)
3:46735377 (GRCh37)
Canonical SPDI:: NC_000003.12:46693886:C:T
Gene:: ALS2CL (Varview), TMIE (Varview)
Functional Consequence:: 5_prime_UTR_variant,upstream_transcript_variant,2KB_upstream_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000014/2 (GnomAD)
T=0.000015/4 (TOPMED)
HGVS:: NC_000003.12:g.46693887C>T, NC_000003.11:g.46735377C>T, NM_001370524.1:c.-798C>T, NM_001370525.1:c.-488C>T

Select item 148904728220.

rs1489047282 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 3:46693203 (GRCh38)
3:46734693 (GRCh37)
Canonical SPDI:: NC_000003.12:46693202:T:C
Gene:: ALS2CL (Varview), TMIE (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
C=0.000007/1 (GnomAD)
HGVS:: NC_000003.12:g.46693203T>C, NC_000003.11:g.46734693T>C

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