HSPA4 - SNP

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Select item 617496311.

rs61749631 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 5:133101807 (GRCh38)
5:132437499 (GRCh37)
Canonical SPDI:: NC_000005.10:133101806:C:T
Gene:: HSPA4 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.009267/1997 (ALFA)
T=0.000342/1 (KOREAN)
T=0.002109/166 (PAGE_STUDY)
T=0.002186/11 (1000Genomes)
T=0.003745/2 (MGP)
T=0.005542/1467 (TOPMED)
T=0.006345/1578 (GnomAD_exomes)
T=0.006579/2 (FINRISK)
T=0.006901/965 (GnomAD)
T=0.007124/862 (ExAC)
T=0.008381/109 (GoESP)
T=0.00986/38 (ALSPAC)
T=0.011597/43 (TWINSUK)
T=0.013026/13 (GoNL)
T=0.015/9 (NorthernSweden)
T=0.017411/78 (Estonian)
T=0.05/2 (GENOME_DK)
HGVS:: NC_000005.10:g.133101807C>T, NC_000005.9:g.132437499C>T, NM_002154.4:c.2086C>T, NM_002154.3:c.2086C>T, NP_002145.3:p.Pro696Ser

Select item 617557232.

rs61755723 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 5:133099561 (GRCh38)
5:132435253 (GRCh37)
Canonical SPDI:: NC_000005.10:133099560:C:G
Gene:: HSPA4 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.004933/243 (ALFA)
G=0.002004/2 (GoNL)
G=0.003289/1 (FINRISK)
G=0.003333/2 (NorthernSweden)
G=0.003776/14 (TWINSUK)
G=0.004229/55 (GoESP)
G=0.004415/619 (GnomAD)
G=0.004432/1173 (TOPMED)
G=0.005667/1420 (GnomAD_exomes)
G=0.005834/706 (ExAC)
G=0.007027/35 (1000Genomes)
G=0.007525/29 (ALSPAC)
G=0.008482/38 (Estonian)
G=0.013109/7 (MGP)
C=0.5/1 (Siberian)
C=0.5/2 (SGDP_PRJ)
HGVS:: NC_000005.10:g.133099561C>G, NC_000005.9:g.132435253C>G, NM_002154.4:c.1946C>G, NM_002154.3:c.1946C>G, NP_002145.3:p.Thr649Ser

Select item 789421853.

rs78942185 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: 5:133076650 (GRCh38)
5:132412342 (GRCh37)
Canonical SPDI:: NC_000005.10:133076649:T:A
Gene:: HSPA4 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.005337/239 (ALFA)
A=0./0 (TWINSUK)
A=0.000259/1 (ALSPAC)
A=0.00463/1 (Qatari)
A=0.004885/1221 (GnomAD_exomes)
A=0.006351/763 (ExAC)
A=0.019793/2775 (GnomAD)
A=0.02093/5540 (TOPMED)
A=0.021081/106 (1000Genomes)
A=0.022374/291 (GoESP)
T=0.5/7 (SGDP_PRJ)
HGVS:: NC_000005.10:g.133076650T>A, NC_000005.9:g.132412342T>A

Select item 1159397094.

rs115939709 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,G [Show Flanks]
Chromosome:: 5:133074057 (GRCh38)
5:132409749 (GRCh37)
Canonical SPDI:: NC_000005.10:133074056:A:C,NC_000005.10:133074056:A:G
Gene:: HSPA4 (Varview)
Functional Consequence:: coding_sequence_variant,synonymous_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.005919/336 (ALFA)
G=0.000035/1 (TOMMO)
C=0.00027/1 (TWINSUK)
C=0.000778/3 (ALSPAC)
C=0.005686/1408 (GnomAD_exomes)
C=0.006545/793 (ExAC)
C=0.007491/4 (MGP)
C=0.009259/2 (Qatari)
C=0.018554/2602 (GnomAD)
C=0.018766/244 (GoESP)
C=0.019997/5293 (TOPMED)
C=0.021237/106 (1000Genomes)
A=0.375/3 (SGDP_PRJ)
HGVS:: NC_000005.10:g.133074057A>C, NC_000005.10:g.133074057A>G, NC_000005.9:g.132409749A>C, NC_000005.9:g.132409749A>G, NM_002154.4:c.594A>C, NM_002154.4:c.594A>G, NM_002154.3:c.594A>C, NM_002154.3:c.594A>G

Select item 1164576095.

rs116457609 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:133096088 (GRCh38)
5:132431780 (GRCh37)
Canonical SPDI:: NC_000005.10:133096087:A:G
Gene:: HSPA4 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.00543/153 (ALFA)
G=0.000071/1 (TOMMO)
G=0.002498/13 (1000Genomes)
G=0.003529/934 (TOPMED)
G=0.003767/49 (GoESP)
G=0.005385/755 (GnomAD)
G=0.005394/20 (TWINSUK)
G=0.005449/21 (ALSPAC)
G=0.005981/1479 (GnomAD_exomes)
G=0.00705/755 (ExAC)
G=0.009018/9 (GoNL)
G=0.011607/52 (Estonian)
G=0.013333/8 (NorthernSweden)
G=0.016447/5 (FINRISK)
G=0.025/1 (GENOME_DK)
A=0.5/1 (Siberian)
A=0.5/2 (SGDP_PRJ)
HGVS:: NC_000005.10:g.133096088A>G, NC_000005.9:g.132431780A>G

Select item 1436318356.

rs143631835 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G,T [Show Flanks]
Chromosome:: 5:133052346 (GRCh38)
5:132388038 (GRCh37)
Canonical SPDI:: NC_000005.10:133052345:C:G,NC_000005.10:133052345:C:T
Gene:: HSPA4 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant,synonymous_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.001947/83 (ALFA)
T=0.000468/2 (1000Genomes)
T=0.000773/10 (GoESP)
T=0.001232/326 (TOPMED)
T=0.001247/175 (GnomAD)
T=0.001348/5 (TWINSUK)
T=0.001511/41 (ExAC)
T=0.001667/1 (NorthernSweden)
T=0.002076/8 (ALSPAC)
T=0.00501/5 (GoNL)
HGVS:: NC_000005.10:g.133052346C>G, NC_000005.10:g.133052346C>T, NC_000005.9:g.132388038C>G, NC_000005.9:g.132388038C>T, NM_002154.4:c.96C>G, NM_002154.4:c.96C>T, NM_002154.3:c.96C>G, NM_002154.3:c.96C>T, NM_198431.1:c.96C>G, NM_198431.1:c.96C>T, NP_002145.3:p.Asp32Glu

Select item 1452910967.

rs145291096 [Homo sapiens]

Variant type:: SNV
Alleles:: A>C,G [Show Flanks]
Chromosome:: 5:133073253 (GRCh38)
5:132408945 (GRCh37)
Canonical SPDI:: NC_000005.10:133073252:A:C,NC_000005.10:133073252:A:G
Gene:: HSPA4 (Varview)
Functional Consequence:: coding_sequence_variant,synonymous_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.00004/1 (ALFA)
G=0.00154/20 (GoESP)
G=0.00219/11 (1000Genomes)
HGVS:: NC_000005.10:g.133073253A>C, NC_000005.10:g.133073253A>G, NC_000005.9:g.132408945A>C, NC_000005.9:g.132408945A>G, NM_002154.4:c.453A>C, NM_002154.4:c.453A>G, NM_002154.3:c.453A>C, NM_002154.3:c.453A>G

Select item 1455485428.

rs145548542 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 5:133076816 (GRCh38)
5:132412508 (GRCh37)
Canonical SPDI:: NC_000005.10:133076815:T:C
Gene:: HSPA4 (Varview)
Functional Consequence:: coding_sequence_variant,synonymous_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.000754/34 (ALFA)
C=0.000574/144 (GnomAD_exomes)
C=0.000718/87 (ExAC)
C=0.002629/696 (TOPMED)
C=0.002753/386 (GnomAD)
C=0.002768/36 (GoESP)
C=0.003435/17 (1000Genomes)
HGVS:: NC_000005.10:g.133076816T>C, NC_000005.9:g.132412508T>C, NM_002154.4:c.826T>C, NM_002154.3:c.826T>C

Select item 1853851789.

rs185385178 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:133073328 (GRCh38)
5:132409020 (GRCh37)
Canonical SPDI:: NC_000005.10:133073327:A:G
Gene:: HSPA4 (Varview)
Functional Consequence:: coding_sequence_variant,synonymous_variant
Clinical significance:: likely-benign
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.000061/10 (ALFA)
G=0.000314/44 (GnomAD)
G=0.000336/89 (TOPMED)
G=0.000611/74 (ExAC)
G=0.000672/166 (GnomAD_exomes)
G=0.000684/2 (KOREAN)
G=0.001093/5 (1000Genomes)
G=0.002583/43 (TOMMO)
G=0.002729/5 (Korea1K)
G=0.006313/5 (PRJEB37584)
G=0.014019/3 (Vietnamese)
HGVS:: NC_000005.10:g.133073328A>G, NC_000005.9:g.132409020A>G, NM_002154.4:c.528A>G, NM_002154.3:c.528A>G

Select item 1371810.

rs13718 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:133105610 (GRCh38)
5:132441302 (GRCh37)
Canonical SPDI:: NC_000005.10:133105609:A:G
Gene:: HSPA4 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.225679/57335 (ALFA)
G=0.084906/18 (Vietnamese)
G=0.093566/1568 (TOMMO)
G=0.117722/93 (PRJEB37584)
G=0.124573/365 (KOREAN)
G=0.137009/251 (Korea1K)
G=0.159091/14 (PRJEB36033)
G=0.177734/13988 (PAGE_STUDY)
G=0.190476/360 (HapMap)
G=0.191131/957 (1000Genomes)
G=0.208055/55070 (TOPMED)
G=0.222492/825 (TWINSUK)
G=0.222998/31226 (GnomAD)
G=0.23041/888 (ALSPAC)
G=0.243386/276 (Daghestan)
G=0.248497/248 (GoNL)
G=0.25463/55 (Qatari)
G=0.257812/1155 (Estonian)
G=0.3/180 (NorthernSweden)
G=0.325/13 (GENOME_DK)
A=0.446903/101 (SGDP_PRJ)
A=0.464286/13 (Siberian)
HGVS:: NC_000005.10:g.133105610A>G, NC_000005.9:g.132441302A>G, NM_002154.4:c.*1174A>G

Select item 1435511.

rs14355 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G [Show Flanks]
Chromosome:: 5:133104593 (GRCh38)
5:132440285 (GRCh37)
Canonical SPDI:: NC_000005.10:133104592:C:G
Gene:: HSPA4 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.264551/5309 (ALFA)
G=0.084906/18 (Vietnamese)
G=0.093566/1568 (TOMMO)
G=0.124573/365 (KOREAN)
G=0.137009/251 (Korea1K)
G=0.225309/73 (HapMap)
G=0.226577/1135 (1000Genomes)
G=0.242179/898 (TWINSUK)
G=0.250908/967 (ALSPAC)
G=0.251472/66562 (TOPMED)
G=0.263338/36880 (GnomAD)
G=0.263527/263 (GoNL)
G=0.280357/1256 (Estonian)
G=0.305/183 (NorthernSweden)
G=0.310185/67 (Qatari)
G=0.325/13 (GENOME_DK)
C=0.43985/117 (SGDP_PRJ)
C=0.464286/13 (Siberian)
HGVS:: NC_000005.10:g.133104593C>G, NC_000005.9:g.132440285C>G, NM_002154.4:c.*157C>G, NM_002154.3:c.*157C>G, NM_198431.1:c.*157C>G

PubMed LitVar

Select item 113180912.

rs1131809 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 5:133101839 (GRCh38)
5:132437531 (GRCh37)
Canonical SPDI:: NC_000005.10:133101838:C:T
Gene:: HSPA4 (Varview)
Functional Consequence:: synonymous_variant,coding_sequence_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.230737/14146 (ALFA)
T=0.093673/1570 (TOMMO)
T=0.107143/66 (Vietnamese)
T=0.124573/365 (KOREAN)
T=0.129213/69 (MGP)
T=0.136463/250 (Korea1K)
T=0.168488/844 (1000Genomes)
T=0.188738/49957 (TOPMED)
T=0.204749/28594 (GnomAD)
T=0.209824/51931 (GnomAD_exomes)
T=0.211825/2755 (GoESP)
T=0.217293/26116 (ExAC)
T=0.222222/824 (TWINSUK)
T=0.23015/887 (ALSPAC)
T=0.240741/52 (Qatari)
T=0.248497/248 (GoNL)
T=0.254967/77 (FINRISK)
T=0.258036/1156 (Estonian)
T=0.3/180 (NorthernSweden)
T=0.325/13 (GENOME_DK)
C=0.443925/95 (SGDP_PRJ)
C=0.464286/13 (Siberian)
HGVS:: NC_000005.10:g.133101839C>T, NC_000005.9:g.132437531C>T, NM_002154.4:c.2118C>T, NM_002154.3:c.2118C>T

Select item 113185213.

rs1131852 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 5:133103630 (GRCh38)
5:132439322 (GRCh37)
Canonical SPDI:: NC_000005.10:133103629:C:T
Gene:: HSPA4 (Varview)
Functional Consequence:: intron_variant
Validated:: by cluster
HGVS:: NC_000005.10:g.133103630C>T, NC_000005.9:g.132439322C>T

Select item 113336314.

rs1133363 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 5:133106163 (GRCh38)
5:132441855 (GRCh37)
Canonical SPDI:: NC_000005.10:133106162:G:T
Gene:: HSPA4 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000337/4 (ALFA)
T=0.000063/7 (GnomAD)
T=0.000286/5 (TOMMO)
T=0.014051/41 (KOREAN)
HGVS:: NC_000005.10:g.133106163G>T, NC_000005.9:g.132441855G>T, NM_002154.4:c.*1727G>T

Select item 114067715.

rs1140677 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,T [Show Flanks]
Chromosome:: 5:133052072 (GRCh38)
5:132387764 (GRCh37)
Canonical SPDI:: NC_000005.10:133052071:C:A,NC_000005.10:133052071:C:T
Gene:: HSPA4 (Varview)
Functional Consequence:: 5_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000015/4 (TOPMED)
T=0.000029/4 (GnomAD)
HGVS:: NC_000005.10:g.133052072C>A, NC_000005.10:g.133052072C>T, NC_000005.9:g.132387764C>A, NC_000005.9:g.132387764C>T, NM_002154.4:c.-179C>A, NM_002154.4:c.-179C>T, NM_002154.3:c.-179C>A, NM_002154.3:c.-179C>T, NM_198431.1:c.-179C>A, NM_198431.1:c.-179C>T

Select item 308822516.

rs3088225 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:133051568 (GRCh38)
5:132387260 (GRCh37)
Canonical SPDI:: NC_000005.10:133051567:A:G
Gene:: HSPA4 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.270031/61439 (ALFA)
G=0.245685/911 (TWINSUK)
G=0.254281/980 (ALSPAC)
G=0.265531/265 (GoNL)
G=0.287277/1287 (Estonian)
G=0.305/183 (NorthernSweden)
G=0.325/13 (GENOME_DK)
G=0.341602/5725 (TOMMO)
A=0.34375/11 (Siberian)
G=0.362931/50790 (GnomAD)
G=0.363208/77 (Vietnamese)
G=0.364868/96577 (TOPMED)
G=0.375/81 (Qatari)
A=0.381356/135 (SGDP_PRJ)
G=0.38273/1917 (1000Genomes)
G=0.391921/718 (Korea1K)
G=0.397952/1166 (KOREAN)
G=0.413329/32524 (PAGE_STUDY)
G=0.434183/818 (HapMap)
G=0.440657/349 (PRJEB37584)
HGVS:: NC_000005.10:g.133051568A>G, NC_000005.9:g.132387260A>G

PubMed

Select item 393511917.

rs3935119 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 5:133057648 (GRCh38)
5:132393340 (GRCh37)
Canonical SPDI:: NC_000005.10:133057647:A:G
Gene:: HSPA4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.231657/4376 (ALFA)
G=0.084112/18 (Vietnamese)
G=0.093602/1569 (TOMMO)
G=0.124573/365 (KOREAN)
G=0.137009/251 (Korea1K)
G=0.190506/954 (1000Genomes)
G=0.207983/55051 (TOPMED)
G=0.221953/823 (TWINSUK)
G=0.222983/31244 (GnomAD)
G=0.23041/888 (ALSPAC)
G=0.249499/249 (GoNL)
G=0.25463/55 (Qatari)
G=0.257366/1153 (Estonian)
G=0.3/180 (NorthernSweden)
G=0.325/13 (GENOME_DK)
A=0.446429/100 (SGDP_PRJ)
A=0.464286/13 (Siberian)
HGVS:: NC_000005.10:g.133057648A>G, NC_000005.9:g.132393340A>G

Select item 412834418.

rs4128344 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G,T [Show Flanks]
Chromosome:: 5:133082388 (GRCh38)
5:132418080 (GRCh37)
Canonical SPDI:: NC_000005.10:133082387:C:G,NC_000005.10:133082387:C:T
Gene:: HSPA4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.121788/1725 (ALFA)
G=0.083333/18 (Vietnamese)
G=0.094203/1579 (TOMMO)
G=0.125256/367 (KOREAN)
G=0.136463/250 (Korea1K)
G=0.191131/957 (1000Genomes)
G=0.208467/55179 (TOPMED)
G=0.221953/823 (TWINSUK)
G=0.23015/887 (ALSPAC)
G=0.248497/248 (GoNL)
G=0.25463/55 (Qatari)
G=0.257143/1152 (Estonian)
G=0.3/180 (NorthernSweden)
G=0.325/13 (GENOME_DK)
C=0.446903/101 (SGDP_PRJ)
C=0.464286/13 (Siberian)
HGVS:: NC_000005.10:g.133082388C>G, NC_000005.10:g.133082388C>T, NC_000005.9:g.132418080C>G, NC_000005.9:g.132418080C>T

Select item 427359719.

rs4273597 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 5:133086102 (GRCh38)
5:132421794 (GRCh37)
Canonical SPDI:: NC_000005.10:133086101:C:A
Gene:: HSPA4 (Varview)
Functional Consequence:: intron_variant
Validated:: by cluster
HGVS:: NC_000005.10:g.133086102C>A, NC_000005.9:g.132421794C>A

Select item 430122920.

rs4301229 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 5:133099796 (GRCh38)
5:132435488 (GRCh37)
Canonical SPDI:: NC_000005.10:133099795:C:T
Gene:: HSPA4 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.229963/4344 (ALFA)
T=0.046816/25 (MGP)
T=0.084906/18 (Vietnamese)
T=0.093637/1569 (TOMMO)
T=0.121406/76 (Chileans)
T=0.124573/365 (KOREAN)
T=0.137009/251 (Korea1K)
T=0.185197/927 (1000Genomes)
T=0.203472/53857 (TOPMED)
T=0.218892/30644 (GnomAD)
T=0.222222/824 (TWINSUK)
T=0.23015/887 (ALSPAC)
T=0.248497/248 (GoNL)
T=0.25463/55 (Qatari)
T=0.257812/1155 (Estonian)
T=0.3/180 (NorthernSweden)
T=0.325/13 (GENOME_DK)
C=0.446903/101 (SGDP_PRJ)
C=0.464286/13 (Siberian)
HGVS:: NC_000005.10:g.133099796C>T, NC_000005.9:g.132435488C>T

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