SNP Links for Gene (Select 152519) - SNP

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Select item 14915241431.

rs1491524143 [Homo sapiens]

Variant type:: DELINS
Alleles:: AT>- [Show Flanks]
Chromosome:: 4:48036093 (GRCh38)
4:48038110 (GRCh37)
Canonical SPDI:: NC_000004.12:48036091:TAT:T
Gene:: NIPAL1 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,frameshift_variant,coding_sequence_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000447/2 (ALFA)
-=0.000008/1 (ExAC)
-=0.000008/2 (GnomAD_exomes)
-=0.000446/2 (Estonian)
HGVS:: NC_000004.12:g.48036093_48036094del, NC_000004.11:g.48038110_48038111del, NM_207330.3:c.1154_1155del, NM_207330.2:c.1154_1155del, NM_207330.1:c.1154_1155del, XM_017007784.2:c.785_786del, XM_017007784.1:c.785_786del, NP_997213.1:p.Tyr385fs, XP_016863273.1:p.Tyr262fs

Select item 14913294972.

rs1491329497 has merged into rs67279375 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTTTT>-,T,TT,TTT,TTTT,TTTTTT [Show Flanks]
Chromosome:: 4:48026732 (GRCh38)
4:48028749 (GRCh37)
Canonical SPDI:: NC_000004.12:48026720:TTTTTTTTTTTTTTTT:TTTTTTTTTTT,NC_000004.12:48026720:TTTTTTTTTTTTTTTT:TTTTTTTTTTTT,NC_000004.12:48026720:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTT,NC_000004.12:48026720:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTT,NC_000004.12:48026720:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTT,NC_000004.12:48026720:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT
Gene:: NIPAL1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTTTTT=0./0 (ALFA)
-=0.000008/2 (TOPMED)
HGVS:: NC_000004.12:g.48026732_48026736del, NC_000004.12:g.48026733_48026736del, NC_000004.12:g.48026734_48026736del, NC_000004.12:g.48026735_48026736del, NC_000004.12:g.48026736del, NC_000004.12:g.48026736dup, NC_000004.11:g.48028749_48028753del, NC_000004.11:g.48028750_48028753del, NC_000004.11:g.48028751_48028753del, NC_000004.11:g.48028752_48028753del, NC_000004.11:g.48028753del, NC_000004.11:g.48028753dup

Select item 14910393843.

rs1491039384 has merged into rs368297289 [Homo sapiens]

Variant type:: DELINS
Alleles:: AAA>-,A,AA,AAAA,AAAAA,AAAAAA,AAAAAAA,AAAAAAAA [Show Flanks]
Chromosome:: 4:48040585 (GRCh38)
4:48042602 (GRCh37)
Canonical SPDI:: NC_000004.12:48040572:AAAAAAAAAAAAAAA:AAAAAAAAAAAA,NC_000004.12:48040572:AAAAAAAAAAAAAAA:AAAAAAAAAAAAA,NC_000004.12:48040572:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAA,NC_000004.12:48040572:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA,NC_000004.12:48040572:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA,NC_000004.12:48040572:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA,NC_000004.12:48040572:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAA,NC_000004.12:48040572:AAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA
Gene:: NIPAL1 (Varview)
Functional Consequence:: 500B_downstream_variant,downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAAAAAAAAAAAAA=0./0 (ALFA)
HGVS:: NC_000004.12:g.48040585_48040587del, NC_000004.12:g.48040586_48040587del, NC_000004.12:g.48040587del, NC_000004.12:g.48040587dup, NC_000004.12:g.48040586_48040587dup, NC_000004.12:g.48040585_48040587dup, NC_000004.12:g.48040584_48040587dup, NC_000004.12:g.48040583_48040587dup, NC_000004.11:g.48042602_48042604del, NC_000004.11:g.48042603_48042604del, NC_000004.11:g.48042604del, NC_000004.11:g.48042604dup, NC_000004.11:g.48042603_48042604dup, NC_000004.11:g.48042602_48042604dup, NC_000004.11:g.48042601_48042604dup, NC_000004.11:g.48042600_48042604dup

Select item 14909854914.

rs1490985491 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 4:48032645 (GRCh38)
4:48034662 (GRCh37)
Canonical SPDI:: NC_000004.12:48032644:A:G
Gene:: NIPAL1 (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_000004.12:g.48032645A>G, NC_000004.11:g.48034662A>G

Select item 14907324955.

rs1490732495 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 4:48023948 (GRCh38)
4:48025965 (GRCh37)
Canonical SPDI:: NC_000004.12:48023947:C:T
Gene:: NIPAL1 (Varview)
Functional Consequence:: intron_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_000004.12:g.48023948C>T, NC_000004.11:g.48025965C>T

Select item 14907171156.

rs1490717115 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 4:48020560 (GRCh38)
4:48022577 (GRCh37)
Canonical SPDI:: NC_000004.12:48020559:G:T
Gene:: NIPAL1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000224/1 (ALFA)
T=0.000007/1 (GnomAD)
T=0.000223/1 (Estonian)
HGVS:: NC_000004.12:g.48020560G>T, NC_000004.11:g.48022577G>T

Select item 14905981977.

rs1490598197 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 4:48022262 (GRCh38)
4:48024279 (GRCh37)
Canonical SPDI:: NC_000004.12:48022261:T:A
Gene:: NIPAL1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000071/1 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000008/2 (TOPMED)
HGVS:: NC_000004.12:g.48022262T>A, NC_000004.11:g.48024279T>A

Select item 14905261828.

rs1490526182 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 4:48040344 (GRCh38)
4:48042361 (GRCh37)
Canonical SPDI:: NC_000004.12:48040343:G:A
Gene:: NIPAL1 (Varview)
Functional Consequence:: 500B_downstream_variant,downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000084/1 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000011/3 (TOPMED)
A=0.000035/1 (TOMMO)
G=0.5/1 (SGDP_PRJ)
HGVS:: NC_000004.12:g.48040344G>A, NC_000004.11:g.48042361G>A

Select item 14905125109.

rs1490512510 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 4:48034835 (GRCh38)
4:48036852 (GRCh37)
Canonical SPDI:: NC_000004.12:48034834:A:G
Gene:: NIPAL1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by cluster
MAF:: G=0.000004/1 (GnomAD_exomes)
G=0.000007/1 (GnomAD)
HGVS:: NC_000004.12:g.48034835A>G, NC_000004.11:g.48036852A>G

Select item 149024270010.

rs1490242700 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 4:48024382 (GRCh38)
4:48026399 (GRCh37)
Canonical SPDI:: NC_000004.12:48024381:G:A
Gene:: NIPAL1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000011/3 (TOPMED)
A=0.000156/1 (1000Genomes)
HGVS:: NC_000004.12:g.48024382G>A, NC_000004.11:g.48026399G>A

Select item 149004773311.

rs1490047733 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 4:48016374 (GRCh38)
4:48018391 (GRCh37)
Canonical SPDI:: NC_000004.12:48016373:G:C
Gene:: CNGA1 (Varview), NIPAL1 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,genic_upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
C=0.000019/5 (TOPMED)
HGVS:: NC_000004.12:g.48016374G>C, NC_000004.11:g.48018391G>C, NG_009193.1:g.1571C>G

Select item 148983955212.

rs1489839552 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 4:48033287 (GRCh38)
4:48035304 (GRCh37)
Canonical SPDI:: NC_000004.12:48033286:T:C
Gene:: NIPAL1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000008/2 (TOPMED)
HGVS:: NC_000004.12:g.48033287T>C, NC_000004.11:g.48035304T>C

Select item 148982731213.

rs1489827312 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 4:48016753 (GRCh38)
4:48018770 (GRCh37)
Canonical SPDI:: NC_000004.12:48016752:C:T
Gene:: CNGA1 (Varview), NIPAL1 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
HGVS:: NC_000004.12:g.48016753C>T, NC_000004.11:g.48018770C>T, NG_009193.1:g.1192G>A

Select item 148973045714.

rs1489730457 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 4:48016448 (GRCh38)
4:48018465 (GRCh37)
Canonical SPDI:: NC_000004.12:48016447:G:C
Gene:: CNGA1 (Varview), NIPAL1 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,genic_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_000004.12:g.48016448G>C, NC_000004.11:g.48018465G>C, NG_009193.1:g.1497C>G

Select item 148937437115.

rs1489374371 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 4:48025506 (GRCh38)
4:48027523 (GRCh37)
Canonical SPDI:: NC_000004.12:48025505:C:T
Gene:: NIPAL1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000071/1 (ALFA)
T=0.000021/3 (GnomAD)
T=0.000023/6 (TOPMED)
HGVS:: NC_000004.12:g.48025506C>T, NC_000004.11:g.48027523C>T

Select item 148931639816.

rs1489316398 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 4:48023108 (GRCh38)
4:48025125 (GRCh37)
Canonical SPDI:: NC_000004.12:48023107:C:G
Gene:: NIPAL1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: G=0.0121/54 (ALFA)
G=0./0 (KOREAN)
HGVS:: NC_000004.12:g.48023108C>G, NC_000004.11:g.48025125C>G

Select item 148926932717.

rs1489269327 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 4:48016906 (GRCh38)
4:48018923 (GRCh37)
Canonical SPDI:: NC_000004.12:48016905:G:A
Gene:: CNGA1 (Varview), NIPAL1 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
HGVS:: NC_000004.12:g.48016906G>A, NC_000004.11:g.48018923G>A, NG_009193.1:g.1039C>T

Select item 148918993118.

rs1489189931 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 4:48017508 (GRCh38)
4:48019525 (GRCh37)
Canonical SPDI:: NC_000004.12:48017507:G:A
Gene:: CNGA1 (Varview), NIPAL1 (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=0.000007/1 (GnomAD)
HGVS:: NC_000004.12:g.48017508G>A, NC_000004.11:g.48019525G>A, NG_009193.1:g.437C>T

Select item 148900391019.

rs1489003910 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 4:48038010 (GRCh38)
4:48040027 (GRCh37)
Canonical SPDI:: NC_000004.12:48038009:G:T
Gene:: NIPAL1 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,3_prime_UTR_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_000004.12:g.48038010G>T, NC_000004.11:g.48040027G>T, NM_207330.3:c.*1838G>T, NM_207330.2:c.*1838G>T, XM_017007784.2:c.*1838G>T, XM_017007784.1:c.*1838G>T

Select item 148893512920.

rs1488935129 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 4:48022276 (GRCh38)
4:48024293 (GRCh37)
Canonical SPDI:: NC_000004.12:48022275:A:G
Gene:: NIPAL1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.000071/1 (ALFA)
G=0.000029/4 (GnomAD)
G=0.000045/12 (TOPMED)
G=0.000342/1 (KOREAN)
HGVS:: NC_000004.12:g.48022276A>G, NC_000004.11:g.48024293A>G

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