SNP Links for Gene (Select 811) - SNP

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Select item 14914875041.

rs1491487504 has merged into rs58546164 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTT>-,T,TT,TTTT,TTTTT,TTTTTT,TTTTTTT,TTTTTTTT,TTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT [Show Flanks]
Chromosome:: 19:12944105 (GRCh38)
19:13054919 (GRCh37)
Canonical SPDI:: NC_000019.10:12944089:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTT,NC_000019.10:12944089:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTT,NC_000019.10:12944089:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT,NC_000019.10:12944089:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTT,NC_000019.10:12944089:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTT,NC_000019.10:12944089:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTT,NC_000019.10:12944089:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTT,NC_000019.10:12944089:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTTT,NC_000019.10:12944089:TTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Gene:: CALR (Varview), RAD23A (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant,3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTTTTTTTT=0./0 (ALFA)
-=0.0843/325 (ALSPAC)
T=0.475/19 (GENOME_DK)
HGVS:: NC_000019.10:g.12944105_12944107del, NC_000019.10:g.12944106_12944107del, NC_000019.10:g.12944107del, NC_000019.10:g.12944107dup, NC_000019.10:g.12944106_12944107dup, NC_000019.10:g.12944105_12944107dup, NC_000019.10:g.12944104_12944107dup, NC_000019.10:g.12944103_12944107dup, NC_000019.10:g.12944090_12944107T[24]GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT[1], NC_000019.9:g.13054919_13054921del, NC_000019.9:g.13054920_13054921del, NC_000019.9:g.13054921del, NC_000019.9:g.13054921dup, NC_000019.9:g.13054920_13054921dup, NC_000019.9:g.13054919_13054921dup, NC_000019.9:g.13054918_13054921dup, NC_000019.9:g.13054917_13054921dup, NC_000019.9:g.13054904_13054921T[24]GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT[1], NG_029662.1:g.10506_10508del, NG_029662.1:g.10507_10508del, NG_029662.1:g.10508del, NG_029662.1:g.10508dup, NG_029662.1:g.10507_10508dup, NG_029662.1:g.10506_10508dup, NG_029662.1:g.10505_10508dup, NG_029662.1:g.10504_10508dup, NG_029662.1:g.10491_10508T[24]GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT[1], NM_004343.4:c.*192_*194del, NM_004343.4:c.*193_*194del, NM_004343.4:c.*194del, NM_004343.4:c.*194dup, NM_004343.4:c.*193_*194dup, NM_004343.4:c.*192_*194dup, NM_004343.4:c.*191_*194dup, NM_004343.4:c.*190_*194dup, NM_004343.4:c.*177_*194T[24]GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT[1], NM_004343.3:c.*192_*194del, NM_004343.3:c.*193_*194del, NM_004343.3:c.*194del, NM_004343.3:c.*194dup, NM_004343.3:c.*193_*194dup, NM_004343.3:c.*192_*194dup, NM_004343.3:c.*191_*194dup, NM_004343.3:c.*190_*194dup, NM_004343.3:c.*177_*194T[24]GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT[1]

Select item 14913805432.

rs1491380543 [Homo sapiens]

Variant type:: INS
Alleles:: ->TA,TG [Show Flanks]
Chromosome:: 19:12944548 (GRCh38)
19:13055363 (GRCh37)
Canonical SPDI:: NC_000019.10:12944548::TA,NC_000019.10:12944548::TG
Gene:: CALR (Varview), RAD23A (Varview)
Functional Consequence:: 2KB_upstream_variant,downstream_transcript_variant,upstream_transcript_variant,500B_downstream_variant
Validated:: by frequency,by alfa
MAF:: TG=0./0 (ALFA)
TG=0.00003/2 (GnomAD)
HGVS:: NC_000019.10:g.12944548_12944549insTA, NC_000019.10:g.12944548_12944549insTG, NC_000019.9:g.13055362_13055363insTA, NC_000019.9:g.13055362_13055363insTG, NG_029662.1:g.10949_10950insTA, NG_029662.1:g.10949_10950insTG

Select item 14912892223.

rs1491289222 [Homo sapiens]

Variant type:: DEL
Alleles:: TG>- [Show Flanks]
Chromosome:: 19:12944548 (GRCh38)
19:13055362 (GRCh37)
Canonical SPDI:: NC_000019.10:12944547:TG:
Gene:: CALR (Varview), RAD23A (Varview)
Functional Consequence:: 2KB_upstream_variant,downstream_transcript_variant,upstream_transcript_variant,500B_downstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: -=0./0 (ALFA)
-=0.00011/2 (TOMMO)
HGVS:: NC_000019.10:g.12944548_12944549del, NC_000019.9:g.13055362_13055363del, NG_029662.1:g.10949_10950del

Select item 14912829014.

rs1491282901 [Homo sapiens]

Variant type:: DEL
Alleles:: CT>- [Show Flanks]
Chromosome:: 19:12944089 (GRCh38)
19:13054903 (GRCh37)
Canonical SPDI:: NC_000019.10:12944088:CT:
Gene:: CALR (Varview), RAD23A (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,3_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: -=0./0 (ALFA)
HGVS:: NC_000019.10:g.12944089_12944090del, NC_000019.9:g.13054903_13054904del, NG_029662.1:g.10490_10491del, NM_004343.4:c.*176_*177del, NM_004343.3:c.*176_*177del

Select item 14911060905.

rs1491106090 [Homo sapiens]

Variant type:: INS
Alleles:: ->A,C,T [Show Flanks]
Chromosome:: 19:12944549 (GRCh38)
19:13055364 (GRCh37)
Canonical SPDI:: NC_000019.10:12944549::A,NC_000019.10:12944549::C,NC_000019.10:12944549::T
Gene:: CALR (Varview), RAD23A (Varview)
Functional Consequence:: 2KB_upstream_variant,downstream_transcript_variant,upstream_transcript_variant,500B_downstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.00014/2 (TOMMO)
C=0.015/9 (NorthernSweden)
HGVS:: NC_000019.10:g.12944549_12944550insA, NC_000019.10:g.12944549_12944550insC, NC_000019.10:g.12944549_12944550insT, NC_000019.9:g.13055363_13055364insA, NC_000019.9:g.13055363_13055364insC, NC_000019.9:g.13055363_13055364insT, NG_029662.1:g.10950_10951insA, NG_029662.1:g.10950_10951insC, NG_029662.1:g.10950_10951insT

Select item 14909652626.

rs1490965262 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 19:12942543 (GRCh38)
19:13053357 (GRCh37)
Canonical SPDI:: NC_000019.10:12942542:C:T
Gene:: CALR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0.000084/1 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000019.10:g.12942543C>T, NC_000019.9:g.13053357C>T, NG_029662.1:g.8944C>T

Select item 14905822627.

rs1490582262 [Homo sapiens]

Variant type:: DEL
Alleles:: T>- [Show Flanks]
Chromosome:: 19:12944542 (GRCh38)
19:13055356 (GRCh37)
Canonical SPDI:: NC_000019.10:12944541:T:
Gene:: CALR (Varview), RAD23A (Varview)
Functional Consequence:: 2KB_upstream_variant,downstream_transcript_variant,upstream_transcript_variant,500B_downstream_variant
Validated:: by frequency,by alfa
MAF:: -=0./0 (ALFA)
-=0.000047/5 (GnomAD)
HGVS:: NC_000019.10:g.12944542del, NC_000019.9:g.13055356del, NG_029662.1:g.10943del

Select item 14904172268.

rs1490417226 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 19:12940411 (GRCh38)
19:13051225 (GRCh37)
Canonical SPDI:: NC_000019.10:12940410:G:A
Gene:: CALR (Varview), MIR6515 (Varview)
Functional Consequence:: 2KB_upstream_variant,missense_variant,upstream_transcript_variant,coding_sequence_variant
Validated:: by frequency
MAF:: A=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000019.10:g.12940411G>A, NC_000019.9:g.13051225G>A, NG_029662.1:g.6812G>A, NM_004343.4:c.661G>A, NM_004343.3:c.661G>A, NP_004334.1:p.Glu221Lys

Select item 14903955399.

rs1490395539 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 19:12943648 (GRCh38)
19:13054462 (GRCh37)
Canonical SPDI:: NC_000019.10:12943647:C:T
Gene:: CALR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000004/1 (GnomAD_exomes)
T=0.000004/1 (TOPMED)
HGVS:: NC_000019.10:g.12943648C>T, NC_000019.9:g.13054462C>T, NG_029662.1:g.10049C>T

Select item 149024714210.

rs1490247142 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,G [Show Flanks]
Chromosome:: 19:12944328 (GRCh38)
19:13055142 (GRCh37)
Canonical SPDI:: NC_000019.10:12944327:C:A,NC_000019.10:12944327:C:G
Gene:: CALR (Varview), RAD23A (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000007/1 (GnomAD)
G=0.000008/2 (TOPMED)
A=0.000156/1 (1000Genomes)
HGVS:: NC_000019.10:g.12944328C>A, NC_000019.10:g.12944328C>G, NC_000019.9:g.13055142C>A, NC_000019.9:g.13055142C>G, NG_029662.1:g.10729C>A, NG_029662.1:g.10729C>G, NM_004343.4:c.*415C>A, NM_004343.4:c.*415C>G, NM_004343.3:c.*415C>A, NM_004343.3:c.*415C>G

Select item 149009305611.

rs1490093056 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 19:12939499 (GRCh38)
19:13050313 (GRCh37)
Canonical SPDI:: NC_000019.10:12939498:C:T
Gene:: CALR (Varview), MIR6515 (Varview)
Functional Consequence:: 2KB_upstream_variant,stop_gained,upstream_transcript_variant,coding_sequence_variant
Validated:: by frequency
MAF:: T=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000019.10:g.12939499C>T, NC_000019.9:g.13050313C>T, NG_029662.1:g.5900C>T, NM_004343.4:c.265C>T, NM_004343.3:c.265C>T, NP_004334.1:p.Gln89Ter

Select item 148930572712.

rs1489305727 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 19:12938026 (GRCh38)
19:13048840 (GRCh37)
Canonical SPDI:: NC_000019.10:12938025:G:A
Gene:: CALR (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000011/3 (TOPMED)
HGVS:: NC_000019.10:g.12938026G>A, NC_000019.9:g.13048840G>A, NG_029662.1:g.4427G>A

Select item 148923516013.

rs1489235160 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: 19:12941093 (GRCh38)
19:13051907 (GRCh37)
Canonical SPDI:: NC_000019.10:12941092:G:A,NC_000019.10:12941092:G:C
Gene:: CALR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.00011/2 (TOMMO)
C=0.00055/1 (Korea1K)
HGVS:: NC_000019.10:g.12941093G>A, NC_000019.10:g.12941093G>C, NC_000019.9:g.13051907G>A, NC_000019.9:g.13051907G>C, NG_029662.1:g.7494G>A, NG_029662.1:g.7494G>C

Select item 148875633214.

rs1488756332 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 19:12939116 (GRCh38)
19:13049930 (GRCh37)
Canonical SPDI:: NC_000019.10:12939115:C:T
Gene:: CALR (Varview), MIR6515 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,intron_variant
Validated:: by frequency
MAF:: T=0.000005/1 (GnomAD_exomes)
HGVS:: NC_000019.10:g.12939116C>T, NC_000019.9:g.13049930C>T, NG_029662.1:g.5517C>T

Select item 148844826315.

rs1488448263 has merged into rs1265773065 [Homo sapiens]

Variant type:: DELINS
Alleles:: T>-,TTT [Show Flanks]
Chromosome:: 19:12941204 (GRCh38)
19:13052018 (GRCh37)
Canonical SPDI:: NC_000019.10:12941203:TTT:TT,NC_000019.10:12941203:TTT:TTTTT
Gene:: CALR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTT=0./0 (ALFA)
-=0.000036/5 (GnomAD)
HGVS:: NC_000019.10:g.12941206del, NC_000019.10:g.12941205_12941206dup, NC_000019.9:g.13052020del, NC_000019.9:g.13052019_13052020dup, NG_029662.1:g.7607del, NG_029662.1:g.7606_7607dup

Select item 148792117816.

rs1487921178 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 19:12940499 (GRCh38)
19:13051313 (GRCh37)
Canonical SPDI:: NC_000019.10:12940498:A:C
Gene:: CALR (Varview), MIR6515 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency
MAF:: C=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000019.10:g.12940499A>C, NC_000019.9:g.13051313A>C, NG_029662.1:g.6900A>C, NR_106770.1:n.16A>C

Select item 148676449717.

rs1486764497 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 19:12939094 (GRCh38)
19:13049908 (GRCh37)
Canonical SPDI:: NC_000019.10:12939093:G:A
Gene:: CALR (Varview), MIR6515 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000011/3 (TOPMED)
HGVS:: NC_000019.10:g.12939094G>A, NC_000019.9:g.13049908G>A, NG_029662.1:g.5495G>A

Select item 148666114218.

rs1486661142 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 19:12938526 (GRCh38)
19:13049340 (GRCh37)
Canonical SPDI:: NC_000019.10:12938525:G:A
Gene:: CALR (Varview), MIR6515 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_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_000019.10:g.12938526G>A, NC_000019.9:g.13049340G>A, NG_029662.1:g.4927G>A, NG_068134.1:g.416G>A

Select item 148650526419.

rs1486505264 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,T [Show Flanks]
Chromosome:: 19:12942613 (GRCh38)
19:13053427 (GRCh37)
Canonical SPDI:: NC_000019.10:12942612:A:C,NC_000019.10:12942612:A:T
Gene:: CALR (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000169/2 (ALFA)
T=0.000047/6 (GnomAD)
T=0.001711/5 (KOREAN)
HGVS:: NC_000019.10:g.12942613A>C, NC_000019.10:g.12942613A>T, NC_000019.9:g.13053427A>C, NC_000019.9:g.13053427A>T, NG_029662.1:g.9014A>C, NG_029662.1:g.9014A>T

Select item 148649540620.

rs1486495406 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,T [Show Flanks]
Chromosome:: 19:12940819 (GRCh38)
19:13051633 (GRCh37)
Canonical SPDI:: NC_000019.10:12940818:G:A,NC_000019.10:12940818:G:T
Gene:: CALR (Varview), MIR6515 (Varview)
Functional Consequence:: downstream_transcript_variant,missense_variant,coding_sequence_variant,stop_gained,500B_downstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000043/1 (ALFA)
A=0.000004/1 (GnomAD_exomes)
A=0.000007/1 (GnomAD)
A=0.000035/1 (TOMMO)
HGVS:: NC_000019.10:g.12940819G>A, NC_000019.10:g.12940819G>T, NC_000019.9:g.13051633G>A, NC_000019.9:g.13051633G>T, NG_029662.1:g.7220G>A, NG_029662.1:g.7220G>T, NM_004343.4:c.892G>A, NM_004343.4:c.892G>T, NM_004343.3:c.892G>A, NM_004343.3:c.892G>T, NP_004334.1:p.Glu298Lys, NP_004334.1:p.Glu298Ter

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