SNP Links for Gene (Select 808) - SNP

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Select item 14915677561.

rs1491567756 [Homo sapiens]

Variant type:: DEL
Alleles:: AA>- [Show Flanks]
Chromosome:: 19:46607863 (GRCh38)
19:47111120 (GRCh37)
Canonical SPDI:: NC_000019.10:46607862:AA:
Gene:: CALM3 (Varview), LOC124904729 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency,by alfa
MAF:: -=0./0 (ALFA)
HGVS:: NC_000019.10:g.46607863_46607864del, NC_000019.9:g.47111120_47111121del, NG_051331.1:g.11790_11791del, XR_007067276.1:n.1205_1206del

Select item 14914303562.

rs1491430356 has merged into rs34621966 [Homo sapiens]

Variant type:: DELINS
Alleles:: TTTTTTT>-,TTT,TTTT,TTTTT,TTTTTT,TTTTTTTT,TTTTTTTTT,TTTTTTTTTT,TTTTTTTTTTT,TTTTTTTTTTTTTTTTTT [Show Flanks]
Chromosome:: 19:46604557 (GRCh38)
19:47107814 (GRCh37)
Canonical SPDI:: NC_000019.10:46604547:TTTTTTTTTTTTTTTT:TTTTTTTTT,NC_000019.10:46604547:TTTTTTTTTTTTTTTT:TTTTTTTTTTTT,NC_000019.10:46604547:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTT,NC_000019.10:46604547:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTT,NC_000019.10:46604547:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTT,NC_000019.10:46604547:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTT,NC_000019.10:46604547:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTT,NC_000019.10:46604547:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTT,NC_000019.10:46604547:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTT,NC_000019.10:46604547:TTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTTTTTTTT
Gene:: CALM3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: TTTTTTTTTTTTT=0./0 (ALFA)
T=0.4561/2284 (1000Genomes)
-=0.475/19 (GENOME_DK)
HGVS:: NC_000019.10:g.46604557_46604563del, NC_000019.10:g.46604560_46604563del, NC_000019.10:g.46604561_46604563del, NC_000019.10:g.46604562_46604563del, NC_000019.10:g.46604563del, NC_000019.10:g.46604563dup, NC_000019.10:g.46604562_46604563dup, NC_000019.10:g.46604561_46604563dup, NC_000019.10:g.46604560_46604563dup, NC_000019.10:g.46604553_46604563dup, NC_000019.9:g.47107814_47107820del, NC_000019.9:g.47107817_47107820del, NC_000019.9:g.47107818_47107820del, NC_000019.9:g.47107819_47107820del, NC_000019.9:g.47107820del, NC_000019.9:g.47107820dup, NC_000019.9:g.47107819_47107820dup, NC_000019.9:g.47107818_47107820dup, NC_000019.9:g.47107817_47107820dup, NC_000019.9:g.47107810_47107820dup, NG_051331.1:g.8484_8490del, NG_051331.1:g.8487_8490del, NG_051331.1:g.8488_8490del, NG_051331.1:g.8489_8490del, NG_051331.1:g.8490del, NG_051331.1:g.8490dup, NG_051331.1:g.8489_8490dup, NG_051331.1:g.8488_8490dup, NG_051331.1:g.8487_8490dup, NG_051331.1:g.8480_8490dup

Select item 14912396043.

rs1491239604 [Homo sapiens]

Variant type:: INS
Alleles:: ->GGGAGAAGTCATTTC,GGGAGGGTTCATTTCATCATTTC [Show Flanks]
Chromosome:: 19:46607863 (GRCh38)
19:47111121 (GRCh37)
Canonical SPDI:: NC_000019.10:46607863::GGGAGAAGTCATTTC,NC_000019.10:46607863::GGGAGGGTTCATTTCATCATTTC
Gene:: CALM3 (Varview), LOC124904729 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GGGAGGGTTCATTTCATCATTTC=0./0 (ALFA)
GGGAGAAGTCATTTC=0.00004/1 (TOMMO)
GGGAGGGTTCATTTCATCATTTC=0.00022/2 (GnomAD)
HGVS:: NC_000019.10:g.46607863_46607864insGGGAGAAGTCATTTC, NC_000019.10:g.46607863_46607864insGGGAGGGTTCATTTCATCATTTC, NC_000019.9:g.47111120_47111121insGGGAGAAGTCATTTC, NC_000019.9:g.47111120_47111121insGGGAGGGTTCATTTCATCATTTC, NG_051331.1:g.11790_11791insGGGAGAAGTCATTTC, NG_051331.1:g.11790_11791insGGGAGGGTTCATTTCATCATTTC, XR_007067276.1:n.1205_1206insGAAATGACTTCTCCC, XR_007067276.1:n.1205_1206insGAAATGATGAAATGAACCCTCCC

Select item 14909382794.

rs1490938279 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 19:46604987 (GRCh38)
19:47108244 (GRCh37)
Canonical SPDI:: NC_000019.10:46604986:A:C
Gene:: CALM3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: C=0.01214/144 (ALFA)
C=0.012/35 (KOREAN)
HGVS:: NC_000019.10:g.46604987A>C, NC_000019.9:g.47108244A>C, NG_051331.1:g.8914A>C

Select item 14905210485.

rs1490521048 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 19:46602219 (GRCh38)
19:47105476 (GRCh37)
Canonical SPDI:: NC_000019.10:46602218:G:T
Gene:: CALM3 (Varview), PPP5D1P (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.46602219G>T, NC_000019.9:g.47105476G>T, NG_051331.1:g.6146G>T

Select item 14900301666.

rs1490030166 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 19:46600896 (GRCh38)
19:47104153 (GRCh37)
Canonical SPDI:: NC_000019.10:46600895:G:A
Gene:: CALM3 (Varview), PPP5D1P (Varview)
Functional Consequence:: non_coding_transcript_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency
MAF:: A=0.000007/1 (GnomAD_exomes)
HGVS:: NC_000019.10:g.46600896G>A, NC_000019.9:g.47104153G>A, NG_051331.1:g.4823G>A, NM_001363873.1:c.74C>T, NR_172902.1:n.21C>T, NM_001370551.1:c.-50C>T, NM_001205281.1:c.74C>T, NR_172903.1:n.21C>T, NM_001370550.1:c.-50C>T

Select item 14899894297.

rs1489989429 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 19:46610554 (GRCh38)
19:47113811 (GRCh37)
Canonical SPDI:: NC_000019.10:46610553:A:G
Gene:: CALM3 (Varview), PTGIR (Varview), LOC124904729 (Varview)
Functional Consequence:: 2KB_upstream_variant,500B_downstream_variant,downstream_transcript_variant,upstream_transcript_variant,3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.000216/4 (ALFA)
G=0.000047/6 (GnomAD)
G=0.00067/3 (Estonian)
HGVS:: NC_000019.10:g.46610554A>G, NC_000019.9:g.47113811A>G, NG_051331.1:g.14481A>G, NM_005184.4:c.*1401A>G, NM_005184.3:c.*1401A>G, NM_005184.2:c.*1401A>G, NM_001329924.2:c.*1401A>G, NM_001329924.1:c.*1401A>G, NM_001329926.2:c.*1401A>G, NM_001329926.1:c.*1401A>G, NM_001329925.2:c.*1401A>G, NM_001329925.1:c.*1401A>G, NM_001329922.1:c.*1401A>G, NM_001329921.1:c.*1401A>G, NM_001329923.1:c.*1401A>G

Select item 14895185068.

rs1489518506 [Homo sapiens]

Variant type:: DELINS
Alleles:: CT>- [Show Flanks]
Chromosome:: 19:46607202 (GRCh38)
19:47110459 (GRCh37)
Canonical SPDI:: NC_000019.10:46607199:CTCT:CT
Gene:: CALM3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CTCT=0./0 (ALFA)
-=0.000007/1 (GnomAD)
-=0.000015/4 (TOPMED)
HGVS:: NC_000019.10:g.46607200CT[1], NC_000019.9:g.47110457CT[1], NG_051331.1:g.11127CT[1]

Select item 14891817999.

rs1489181799 [Homo sapiens]

Variant type:: DELINS
Alleles:: TCCAC>- [Show Flanks]
Chromosome:: 19:46609118 (GRCh38)
19:47112375 (GRCh37)
Canonical SPDI:: NC_000019.10:46609114:CACTCCAC:CAC
Gene:: CALM3 (Varview), LOC124904729 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CAC=0./0 (ALFA)
-=0.000008/2 (TOPMED)
HGVS:: NC_000019.10:g.46609118_46609122del, NC_000019.9:g.47112375_47112379del, NG_051331.1:g.13045_13049del, XR_007067276.1:n.42_46del

Select item 148860318310.

rs1488603183 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 19:46602978 (GRCh38)
19:47106235 (GRCh37)
Canonical SPDI:: NC_000019.10:46602977:C:G
Gene:: CALM3 (Varview)
Functional Consequence:: 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_000019.10:g.46602978C>G, NC_000019.9:g.47106235C>G, NG_051331.1:g.6905C>G

Select item 148853064011.

rs1488530640 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 19:46603720 (GRCh38)
19:47106977 (GRCh37)
Canonical SPDI:: NC_000019.10:46603719:C:G
Gene:: CALM3 (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_000019.10:g.46603720C>G, NC_000019.9:g.47106977C>G, NG_051331.1:g.7647C>G

Select item 148829065712.

rs1488290657 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 19:46610429 (GRCh38)
19:47113686 (GRCh37)
Canonical SPDI:: NC_000019.10:46610428:T:C
Gene:: CALM3 (Varview), PTGIR (Varview), LOC124904729 (Varview)
Functional Consequence:: 2KB_upstream_variant,500B_downstream_variant,downstream_transcript_variant,upstream_transcript_variant,3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000014/2 (GnomAD)
C=0.000023/6 (TOPMED)
HGVS:: NC_000019.10:g.46610429T>C, NC_000019.9:g.47113686T>C, NG_051331.1:g.14356T>C, NM_005184.4:c.*1276T>C, NM_005184.3:c.*1276T>C, NM_005184.2:c.*1276T>C, NM_001329924.2:c.*1276T>C, NM_001329924.1:c.*1276T>C, NM_001329926.2:c.*1276T>C, NM_001329926.1:c.*1276T>C, NM_001329925.2:c.*1276T>C, NM_001329925.1:c.*1276T>C, NM_001329922.1:c.*1276T>C, NM_001329921.1:c.*1276T>C, NM_001329923.1:c.*1276T>C

Select item 148827645713.

rs1488276457 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 19:46600451 (GRCh38)
19:47103708 (GRCh37)
Canonical SPDI:: NC_000019.10:46600450:G:C
Gene:: CALM3 (Varview), PPP5D1P (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,intron_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_000019.10:g.46600451G>C, NC_000019.9:g.47103708G>C, NG_051331.1:g.4378G>C

Select item 148805745914.

rs1488057459 [Homo sapiens]

Variant type:: DELINS
Alleles:: GAG>- [Show Flanks]
Chromosome:: 19:46603595 (GRCh38)
19:47106852 (GRCh37)
Canonical SPDI:: NC_000019.10:46603592:AGGAG:AG
Gene:: CALM3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: AG=0./0 (ALFA)
-=0.00003/8 (TOPMED)
HGVS:: NC_000019.10:g.46603595_46603597del, NC_000019.9:g.47106852_47106854del, NG_051331.1:g.7522_7524del

Select item 148796120515.

rs1487961205 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 19:46603981 (GRCh38)
19:47107238 (GRCh37)
Canonical SPDI:: NC_000019.10:46603980:C:T
Gene:: CALM3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000023/6 (TOPMED)
HGVS:: NC_000019.10:g.46603981C>T, NC_000019.9:g.47107238C>T, NG_051331.1:g.7908C>T

Select item 148777242116.

rs1487772421 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,T [Show Flanks]
Chromosome:: 19:46608361 (GRCh38)
19:47111618 (GRCh37)
Canonical SPDI:: NC_000019.10:46608360:G:A,NC_000019.10:46608360:G:T
Gene:: CALM3 (Varview), LOC124904729 (Varview)
Functional Consequence:: non_coding_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
HGVS:: NC_000019.10:g.46608361G>A, NC_000019.10:g.46608361G>T, NC_000019.9:g.47111618G>A, NC_000019.9:g.47111618G>T, NG_051331.1:g.12288G>A, NG_051331.1:g.12288G>T, XR_007067276.1:n.708C>T, XR_007067276.1:n.708C>A

Select item 148755212717.

rs1487552127 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 19:46604197 (GRCh38)
19:47107454 (GRCh37)
Canonical SPDI:: NC_000019.10:46604196:C:T
Gene:: CALM3 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000011/3 (TOPMED)
HGVS:: NC_000019.10:g.46604197C>T, NC_000019.9:g.47107454C>T, NG_051331.1:g.8124C>T

Select item 148753168318.

rs1487531683 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 19:46601280 (GRCh38)
19:47104537 (GRCh37)
Canonical SPDI:: NC_000019.10:46601279:A:G
Gene:: CALM3 (Varview), PPP5D1P (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,intron_variant,genic_upstream_transcript_variant
Validated:: by frequency,by cluster
MAF:: G=0.00032/5 (TOMMO)
HGVS:: NC_000019.10:g.46601280A>G, NC_000019.9:g.47104537A>G, NG_051331.1:g.5207A>G, NM_005184.3:c.-155A>G, NM_005184.2:c.-155A>G, NM_001329924.1:c.-261A>G, NM_001329926.1:c.-255A>G, NM_001329925.1:c.-232A>G

Select item 148666056219.

rs1486660562 [Homo sapiens]

Variant type:: DELINS
Alleles:: AGC>- [Show Flanks]
Chromosome:: 19:46602134 (GRCh38)
19:47105391 (GRCh37)
Canonical SPDI:: NC_000019.10:46602131:GCAGC:GC
Gene:: CALM3 (Varview), PPP5D1P (Varview)
Functional Consequence:: 2KB_upstream_variant,5_prime_UTR_variant,upstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GC=0./0 (ALFA)
-=0.000008/2 (TOPMED)
-=0.000014/2 (GnomAD)
HGVS:: NC_000019.10:g.46602134_46602136del, NC_000019.9:g.47105391_47105393del, NG_051331.1:g.6061_6063del, NM_001329922.1:c.-74_-72del

Select item 148655965820.

rs1486559658 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 19:46601570 (GRCh38)
19:47104827 (GRCh37)
Canonical SPDI:: NC_000019.10:46601569:C:T
Gene:: CALM3 (Varview), PPP5D1P (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,intron_variant,genic_upstream_transcript_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_000019.10:g.46601570C>T, NC_000019.9:g.47104827C>T, NG_051331.1:g.5497C>T

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