SNP Links for Gene (Select 4488) - SNP

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Select item 14915187051.

rs1491518705 has merged into rs71310022 [Homo sapiens]

Variant type:: DELINS
Alleles:: AAAAAAAAAAAA>-,AA,AAA,AAAA,AAAAA,AAAAAA,AAAAAAA,AAAAAAAA,AAAAAAAAA,AAAAAAAAAA,AAAAAAAAAAA,AAAAAAAAAAAAA,AAAAAAAAAAAAAA,AAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAAA,AAAAAAAAAAAAAAAAAAA [Show Flanks]
Chromosome:: 5:174724425 (GRCh38)
5:174151428 (GRCh37)
Canonical SPDI:: NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAAAAA,NC_000005.10:174724413:AAAAAAAAAAAAAAAAAAAAAAA:AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Gene:: MSX2 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAAAAAAAA=0./0 (ALFA)
AA=0.225/9 (GENOME_DK)
HGVS:: NC_000005.10:g.174724425_174724436del, NC_000005.10:g.174724427_174724436del, NC_000005.10:g.174724428_174724436del, NC_000005.10:g.174724429_174724436del, NC_000005.10:g.174724430_174724436del, NC_000005.10:g.174724431_174724436del, NC_000005.10:g.174724432_174724436del, NC_000005.10:g.174724433_174724436del, NC_000005.10:g.174724434_174724436del, NC_000005.10:g.174724435_174724436del, NC_000005.10:g.174724436del, NC_000005.10:g.174724436dup, NC_000005.10:g.174724435_174724436dup, NC_000005.10:g.174724434_174724436dup, NC_000005.10:g.174724433_174724436dup, NC_000005.10:g.174724432_174724436dup, NC_000005.10:g.174724431_174724436dup, NC_000005.10:g.174724430_174724436dup, NC_000005.9:g.174151428_174151439del, NC_000005.9:g.174151430_174151439del, NC_000005.9:g.174151431_174151439del, NC_000005.9:g.174151432_174151439del, NC_000005.9:g.174151433_174151439del, NC_000005.9:g.174151434_174151439del, NC_000005.9:g.174151435_174151439del, NC_000005.9:g.174151436_174151439del, NC_000005.9:g.174151437_174151439del, NC_000005.9:g.174151438_174151439del, NC_000005.9:g.174151439del, NC_000005.9:g.174151439dup, NC_000005.9:g.174151438_174151439dup, NC_000005.9:g.174151437_174151439dup, NC_000005.9:g.174151436_174151439dup, NC_000005.9:g.174151435_174151439dup, NC_000005.9:g.174151434_174151439dup, NC_000005.9:g.174151433_174151439dup, NG_008124.1:g.4854_4865del, NG_008124.1:g.4856_4865del, NG_008124.1:g.4857_4865del, NG_008124.1:g.4858_4865del, NG_008124.1:g.4859_4865del, NG_008124.1:g.4860_4865del, NG_008124.1:g.4861_4865del, NG_008124.1:g.4862_4865del, NG_008124.1:g.4863_4865del, NG_008124.1:g.4864_4865del, NG_008124.1:g.4865del, NG_008124.1:g.4865dup, NG_008124.1:g.4864_4865dup, NG_008124.1:g.4863_4865dup, NG_008124.1:g.4862_4865dup, NG_008124.1:g.4861_4865dup, NG_008124.1:g.4860_4865dup, NG_008124.1:g.4859_4865dup

Select item 14914356142.

rs1491435614 [Homo sapiens]

Variant type:: DELINS
Alleles:: AG>- [Show Flanks]
Chromosome:: 5:174723941 (GRCh38)
5:174150944 (GRCh37)
Canonical SPDI:: NC_000005.10:174723935:GAGAGAG:GAGAG
Gene:: MSX2 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GAGAG=0./0 (ALFA)
-=0.000019/5 (TOPMED)
-=0.000036/5 (GnomAD)
HGVS:: NC_000005.10:g.174723937AG[2], NC_000005.9:g.174150940AG[2], NG_008124.1:g.4366AG[2]

Select item 14914013323.

rs1491401332 [Homo sapiens]

Variant type:: INS
Alleles:: ->A,AA [Show Flanks]
Chromosome:: 5:174726585 (GRCh38)
5:174153589 (GRCh37)
Canonical SPDI:: NC_000005.10:174726585::A,NC_000005.10:174726585::AA
Gene:: MSX2 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: AA=0./0 (ALFA)
A=0.00198/56 (TOMMO)
HGVS:: NC_000005.10:g.174726585_174726586insA, NC_000005.10:g.174726585_174726586insAA, NC_000005.9:g.174153588_174153589insA, NC_000005.9:g.174153588_174153589insAA, NG_008124.1:g.7014_7015insA, NG_008124.1:g.7014_7015insAA

Select item 14912932674.

rs1491293267 [Homo sapiens]

Variant type:: DEL
Alleles:: CC>- [Show Flanks]
Chromosome:: 5:174726585 (GRCh38)
5:174153588 (GRCh37)
Canonical SPDI:: NC_000005.10:174726584:CC:
Gene:: MSX2 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: -=0.00007/1 (ALFA)
HGVS:: NC_000005.10:g.174726585_174726586del, NC_000005.9:g.174153588_174153589del, NG_008124.1:g.7014_7015del

Select item 14912421545.

rs1491242154 [Homo sapiens]

Variant type:: DEL
Alleles:: GA>- [Show Flanks]
Chromosome:: 5:174724413 (GRCh38)
5:174151416 (GRCh37)
Canonical SPDI:: NC_000005.10:174724412:GA:
Gene:: MSX2 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: -=0./0 (ALFA)
-=0.00002/1 (GnomAD)
HGVS:: NC_000005.10:g.174724413_174724414del, NC_000005.9:g.174151416_174151417del, NG_008124.1:g.4842_4843del

Select item 14910973516.

rs1491097351 [Homo sapiens]

Variant type:: DEL
Alleles:: CA>- [Show Flanks]
Chromosome:: 5:174726586 (GRCh38)
5:174153589 (GRCh37)
Canonical SPDI:: NC_000005.10:174726585:CA:
Gene:: MSX2 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: -=0./0 (ALFA)
HGVS:: NC_000005.10:g.174726586_174726587del, NC_000005.9:g.174153589_174153590del, NG_008124.1:g.7015_7016del

Select item 14909880877.

rs1490988087 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 5:174729040 (GRCh38)
5:174156043 (GRCh37)
Canonical SPDI:: NC_000005.10:174729039:G:T
Gene:: MSX2 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000011/3 (TOPMED)
HGVS:: NC_000005.10:g.174729040G>T, NC_000005.9:g.174156043G>T, NG_008124.1:g.9469G>T

Select item 14904047528.

rs1490404752 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 5:174727849 (GRCh38)
5:174154852 (GRCh37)
Canonical SPDI:: NC_000005.10:174727848:G:A
Gene:: MSX2 (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_000005.10:g.174727849G>A, NC_000005.9:g.174154852G>A, NG_008124.1:g.8278G>A

Select item 14903187969.

rs1490318796 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 5:174722513 (GRCh38)
5:174149516 (GRCh37)
Canonical SPDI:: NC_000005.10:174722512:T:C
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
HGVS:: NC_000005.10:g.174722513T>C, NC_000005.9:g.174149516T>C, NG_008124.1:g.2942T>C

Select item 148935978210.

rs1489359782 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 5:174726520 (GRCh38)
5:174153523 (GRCh37)
Canonical SPDI:: NC_000005.10:174726519:C:G
Gene:: MSX2 (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_000005.10:g.174726520C>G, NC_000005.9:g.174153523C>G, NG_008124.1:g.6949C>G

Select item 148928425711.

rs1489284257 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->C [Show Flanks]
Chromosome:: 5:174726187 (GRCh38)
5:174153191 (GRCh37)
Canonical SPDI:: NC_000005.10:174726187:CCCCC:CCCCCC
Gene:: MSX2 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: CCCCCC=0./0 (ALFA)
C=0.000011/3 (TOPMED)
HGVS:: NC_000005.10:g.174726192dup, NC_000005.9:g.174153195dup, NG_008124.1:g.6621dup

Select item 148928277212.

rs1489282772 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C,T [Show Flanks]
Chromosome:: 5:174724412 (GRCh38)
5:174151415 (GRCh37)
Canonical SPDI:: NC_000005.10:174724411:G:A,NC_000005.10:174724411:G:C,NC_000005.10:174724411:G:T
Gene:: MSX2 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
A=0.00046/20 (GnomAD)
A=0.03151/92 (KOREAN)
HGVS:: NC_000005.10:g.174724412G>A, NC_000005.10:g.174724412G>C, NC_000005.10:g.174724412G>T, NC_000005.9:g.174151415G>A, NC_000005.9:g.174151415G>C, NC_000005.9:g.174151415G>T, NG_008124.1:g.4841G>A, NG_008124.1:g.4841G>C, NG_008124.1:g.4841G>T

Select item 148910169813.

rs1489101698 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 5:174726106 (GRCh38)
5:174153109 (GRCh37)
Canonical SPDI:: NC_000005.10:174726105:T:A
Gene:: MSX2 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: A=0.000071/1 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000005.10:g.174726106T>A, NC_000005.9:g.174153109T>A, NG_008124.1:g.6535T>A

Select item 148907363214.

rs1489073632 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 5:174724764 (GRCh38)
5:174151767 (GRCh37)
Canonical SPDI:: NC_000005.10:174724763:G:T
Gene:: MSX2 (Varview)
Functional Consequence:: synonymous_variant,coding_sequence_variant
Validated:: by frequency,by cluster
MAF:: T=0.000006/1 (GnomAD_exomes)
HGVS:: NC_000005.10:g.174724764G>T, NC_000005.9:g.174151767G>T, NG_008124.1:g.5193G>T, NM_002449.5:c.105G>T, NM_002449.4:c.105G>T, NM_001363626.2:c.105G>T, NM_001363626.1:c.105G>T

Select item 148872974315.

rs1488729743 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->CTGCT [Show Flanks]
Chromosome:: 5:174729671 (GRCh38)
5:174156675 (GRCh37)
Canonical SPDI:: NC_000005.10:174729671:CTGCTCTGCT:CTGCTCTGCTCTGCT
Gene:: MSX2 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: CTGCTCTGCTCTGCT=0./0 (ALFA)
CTGCT=0.000011/3 (TOPMED)
HGVS:: NC_000005.10:g.174729672CTGCT[3], NC_000005.9:g.174156675CTGCT[3], NG_008124.1:g.10101CTGCT[3], NM_002449.5:c.*89CTGCT[3], NM_002449.4:c.*89CTGCT[3], NM_001363626.2:c.*517CTGCT[3], NM_001363626.1:c.*517CTGCT[3]

Select item 148869862416.

rs1488698624 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A,G [Show Flanks]
Chromosome:: 5:174730507 (GRCh38)
5:174157510 (GRCh37)
Canonical SPDI:: NC_000005.10:174730506:T:A,NC_000005.10:174730506:T:G
Gene:: MSX2 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
HGVS:: NC_000005.10:g.174730507T>A, NC_000005.10:g.174730507T>G, NC_000005.9:g.174157510T>A, NC_000005.9:g.174157510T>G, NG_008124.1:g.10936T>A, NG_008124.1:g.10936T>G, NM_002449.5:c.*924T>A, NM_002449.5:c.*924T>G, NM_002449.4:c.*924T>A, NM_002449.4:c.*924T>G, NM_001363626.2:c.*1352T>A, NM_001363626.2:c.*1352T>G, NM_001363626.1:c.*1352T>A, NM_001363626.1:c.*1352T>G

Select item 148851397417.

rs1488513974 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C [Show Flanks]
Chromosome:: 5:174725857 (GRCh38)
5:174152860 (GRCh37)
Canonical SPDI:: NC_000005.10:174725856:A:C
Gene:: MSX2 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
HGVS:: NC_000005.10:g.174725857A>C, NC_000005.9:g.174152860A>C, NG_008124.1:g.6286A>C

Select item 148807734118.

rs1488077341 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 5:174730397 (GRCh38)
5:174157400 (GRCh37)
Canonical SPDI:: NC_000005.10:174730396:G:A
Gene:: MSX2 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000008/2 (TOPMED)
HGVS:: NC_000005.10:g.174730397G>A, NC_000005.9:g.174157400G>A, NG_008124.1:g.10826G>A, NM_002449.5:c.*814G>A, NM_002449.4:c.*814G>A, NM_001363626.2:c.*1242G>A, NM_001363626.1:c.*1242G>A

Select item 148795493619.

rs1487954936 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 5:174727727 (GRCh38)
5:174154730 (GRCh37)
Canonical SPDI:: NC_000005.10:174727726:C:G
Gene:: MSX2 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000008/2 (TOPMED)
HGVS:: NC_000005.10:g.174727727C>G, NC_000005.9:g.174154730C>G, NG_008124.1:g.8156C>G

Select item 148756177320.

rs1487561773 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 5:174724457 (GRCh38)
5:174151460 (GRCh37)
Canonical SPDI:: NC_000005.10:174724456:G:T
Gene:: MSX2 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
T=0.000008/1 (GnomAD)
HGVS:: NC_000005.10:g.174724457G>T, NC_000005.9:g.174151460G>T, NG_008124.1:g.4886G>T

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