SNP Links for Gene (Select 440957) - SNP

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Select item 14888037991.

rs1488803799 has merged into rs960073319 [Homo sapiens]

Variant type:: DELINS
Alleles:: C>-,CC [Show Flanks]
Chromosome:: 3:52534010 (GRCh38)
3:52568026 (GRCh37)
Canonical SPDI:: NC_000003.12:52534009:CCCCCC:CCCCC,NC_000003.12:52534009:CCCCCC:CCCCCCC
Gene:: NT5DC2 (Varview), LOC124909379 (Varview)
Functional Consequence:: upstream_transcript_variant,genic_upstream_transcript_variant,intron_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CCCCCCC=0./0 (ALFA)
-=0.000107/15 (GnomAD)
HGVS:: NC_000003.12:g.52534015del, NC_000003.12:g.52534015dup, NC_000003.11:g.52568031del, NC_000003.11:g.52568031dup

Select item 14886997112.

rs1488699711 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:52535284 (GRCh38)
3:52569300 (GRCh37)
Canonical SPDI:: NC_000003.12:52535283:G:A
Gene:: NT5DC2 (Varview), SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency
MAF:: A=0.000007/1 (GnomAD)
HGVS:: NC_000003.12:g.52535284G>A, NC_000003.11:g.52569300G>A, NR_003192.1:n.388G>A

Select item 14882783373.

rs1488278337 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,G [Show Flanks]
Chromosome:: 3:52536275 (GRCh38)
3:52570291 (GRCh37)
Canonical SPDI:: NC_000003.12:52536274:A:C,NC_000003.12:52536274:A:G
Gene:: NT5DC2 (Varview), SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.000066/1 (ALFA)
G=0.000004/1 (TOPMED)
G=0.000021/3 (GnomAD)
C=0.000223/1 (Estonian)
HGVS:: NC_000003.12:g.52536275A>C, NC_000003.12:g.52536275A>G, NC_000003.11:g.52570291A>C, NC_000003.11:g.52570291A>G, NR_003192.1:n.1379A>C, NR_003192.1:n.1379A>G

Select item 14877505034.

rs1487750503 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:52540803 (GRCh38)
3:52574819 (GRCh37)
Canonical SPDI:: NC_000003.12:52540802:C:T
Gene:: SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant,3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000142/2 (ALFA)
T=0.000014/2 (GnomAD)
T=0.000049/13 (TOPMED)
HGVS:: NC_000003.12:g.52540803C>T, NC_000003.11:g.52574819C>T, NM_001124767.2:c.*318C>T

Select item 14873607305.

rs1487360730 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 3:52540200 (GRCh38)
3:52574216 (GRCh37)
Canonical SPDI:: NC_000003.12:52540199:T:G
Gene:: SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000007/1 (GnomAD)
G=0.000011/3 (TOPMED)
HGVS:: NC_000003.12:g.52540200T>G, NC_000003.11:g.52574216T>G, NR_003192.1:n.5304T>G

Select item 14873101496.

rs1487310149 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: 3:52534762 (GRCh38)
3:52568778 (GRCh37)
Canonical SPDI:: NC_000003.12:52534761:G:A,NC_000003.12:52534761:G:C
Gene:: NT5DC2 (Varview), SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,5_prime_UTR_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
A=0.000011/3 (TOPMED)
HGVS:: NC_000003.12:g.52534762G>A, NC_000003.12:g.52534762G>C, NC_000003.11:g.52568778G>A, NC_000003.11:g.52568778G>C, NM_022908.3:c.-109C>T, NM_022908.3:c.-109C>G, NM_022908.2:c.-109C>T, NM_022908.2:c.-109C>G, XM_047448760.1:c.-109C>T, XM_047448760.1:c.-109C>G

Select item 14872996047.

rs1487299604 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,G [Show Flanks]
Chromosome:: 3:52537419 (GRCh38)
3:52571435 (GRCh37)
Canonical SPDI:: NC_000003.12:52537418:C:A,NC_000003.12:52537418:C:G
Gene:: SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.000054/1 (ALFA)
A=0./0 (GnomAD)
A=0.000019/5 (TOPMED)
G=0.000223/1 (Estonian)
HGVS:: NC_000003.12:g.52537419C>A, NC_000003.12:g.52537419C>G, NC_000003.11:g.52571435C>A, NC_000003.11:g.52571435C>G, NR_003192.1:n.2523C>A, NR_003192.1:n.2523C>G

Select item 14867422058.

rs1486742205 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:52537766 (GRCh38)
3:52571782 (GRCh37)
Canonical SPDI:: NC_000003.12:52537765:G:A
Gene:: SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
HGVS:: NC_000003.12:g.52537766G>A, NC_000003.11:g.52571782G>A, NR_003192.1:n.2870G>A

Select item 14853389359.

rs1485338935 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:52539732 (GRCh38)
3:52573748 (GRCh37)
Canonical SPDI:: NC_000003.12:52539731:G:A
Gene:: SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
HGVS:: NC_000003.12:g.52539732G>A, NC_000003.11:g.52573748G>A, NR_003192.1:n.4836G>A

Select item 148440904910.

rs1484409049 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:52538714 (GRCh38)
3:52572730 (GRCh37)
Canonical SPDI:: NC_000003.12:52538713:G:A
Gene:: SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000003.12:g.52538714G>A, NC_000003.11:g.52572730G>A, NR_003192.1:n.3818G>A

Select item 148389155911.

rs1483891559 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 3:52537518 (GRCh38)
3:52571534 (GRCh37)
Canonical SPDI:: NC_000003.12:52537517:T:A
Gene:: SMIM4 (Varview), LOC124909379 (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_000003.12:g.52537518T>A, NC_000003.11:g.52571534T>A, NR_003192.1:n.2622T>A

Select item 148339300312.

rs1483393003 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: 3:52540696 (GRCh38)
3:52574712 (GRCh37)
Canonical SPDI:: NC_000003.12:52540695:A:T
Gene:: SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant,3_prime_UTR_variant
HGVS:: NC_000003.12:g.52540696A>T, NC_000003.11:g.52574712A>T, NM_001124767.2:c.*211A>T, NR_003192.1:n.5800A>T

Select item 148265633913.

rs1482656339 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A,C [Show Flanks]
Chromosome:: 3:52536360 (GRCh38)
3:52570376 (GRCh37)
Canonical SPDI:: NC_000003.12:52536359:T:A,NC_000003.12:52536359:T:C
Gene:: NT5DC2 (Varview), SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
HGVS:: NC_000003.12:g.52536360T>A, NC_000003.12:g.52536360T>C, NC_000003.11:g.52570376T>A, NC_000003.11:g.52570376T>C, NR_003192.1:n.1464T>A, NR_003192.1:n.1464T>C

Select item 148259407714.

rs1482594077 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:52535302 (GRCh38)
3:52569318 (GRCh37)
Canonical SPDI:: NC_000003.12:52535301:G:A
Gene:: NT5DC2 (Varview), SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
A=0.000014/2 (GnomAD)
HGVS:: NC_000003.12:g.52535302G>A, NC_000003.11:g.52569318G>A, NR_003192.1:n.406G>A

Select item 148206803715.

rs1482068037 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:52539733 (GRCh38)
3:52573749 (GRCh37)
Canonical SPDI:: NC_000003.12:52539732:G:A
Gene:: SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000003.12:g.52539733G>A, NC_000003.11:g.52573749G>A, NR_003192.1:n.4837G>A

Select item 148200681216.

rs1482006812 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 3:52535735 (GRCh38)
3:52569751 (GRCh37)
Canonical SPDI:: NC_000003.12:52535734:G:C
Gene:: NT5DC2 (Varview), SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
HGVS:: NC_000003.12:g.52535735G>C, NC_000003.11:g.52569751G>C, NR_003192.1:n.839G>C

Select item 148174199817.

rs1481741998 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 3:52535877 (GRCh38)
3:52569893 (GRCh37)
Canonical SPDI:: NC_000003.12:52535876:A:G
Gene:: NT5DC2 (Varview), SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
G=0.000007/1 (GnomAD)
HGVS:: NC_000003.12:g.52535877A>G, NC_000003.11:g.52569893A>G, NR_003192.1:n.981A>G

Select item 148151671618.

rs1481516716 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->A [Show Flanks]
Chromosome:: 3:52534985 (GRCh38)
3:52569002 (GRCh37)
Canonical SPDI:: NC_000003.12:52534985:A:AA
Gene:: NT5DC2 (Varview), SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: upstream_transcript_variant,intron_variant,5_prime_UTR_variant,genic_upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: AA=0./0 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000003.12:g.52534986dup, NC_000003.11:g.52569002dup, NM_022908.3:c.-333dup, NM_022908.2:c.-333dup, NR_003192.1:n.90dup, XM_047448760.1:c.-333dup

Select item 148140974719.

rs1481409747 [Homo sapiens]

Variant type:: DEL
Alleles:: TT>- [Show Flanks]
Chromosome:: 3:52540569 (GRCh38)
3:52574585 (GRCh37)
Canonical SPDI:: NC_000003.12:52540568:TT:
Gene:: SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: 3_prime_UTR_variant,intron_variant
Validated:: by frequency
MAF:: -=0.00001/1 (GnomAD_exomes)
HGVS:: NC_000003.12:g.52540569_52540570del, NC_000003.11:g.52574585_52574586del, NM_001124767.2:c.*84_*85del, NM_001124767.1:c.*84_*85del, NR_003192.1:n.5673_5674del

Select item 148042821720.

rs1480428217 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G,T [Show Flanks]
Chromosome:: 3:52534683 (GRCh38)
3:52568699 (GRCh37)
Canonical SPDI:: NC_000003.12:52534682:C:G,NC_000003.12:52534682:C:T
Gene:: NT5DC2 (Varview), SMIM4 (Varview), LOC124909379 (Varview)
Functional Consequence:: upstream_transcript_variant,5_prime_UTR_variant,2KB_upstream_variant,genic_upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
HGVS:: NC_000003.12:g.52534683C>G, NC_000003.12:g.52534683C>T, NC_000003.11:g.52568699C>G, NC_000003.11:g.52568699C>T, NM_022908.3:c.-30G>C, NM_022908.3:c.-30G>A, NM_022908.2:c.-30G>C, NM_022908.2:c.-30G>A, XM_047448760.1:c.-30G>C, XM_047448760.1:c.-30G>A

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