SNP Links for Gene (Select 7178) - SNP

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Select item 14909789771.

rs1490978977 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 13:45333378 (GRCh38)
13:45907513 (GRCh37)
Canonical SPDI:: NC_000013.11:45333377:C:A
Gene:: TPT1 (Varview)
Functional Consequence:: 500B_downstream_variant,downstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000013.11:g.45333378C>A, NC_000013.10:g.45907513C>A

Select item 14909279332.

rs1490927933 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 13:45334217 (GRCh38)
13:45908352 (GRCh37)
Canonical SPDI:: NC_000013.11:45334216:T:C
Gene:: TPT1 (Varview)
Functional Consequence:: 3_prime_UTR_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_000013.11:g.45334217T>C, NC_000013.10:g.45908352T>C, NM_003295.4:c.*3169A>G, NM_003295.3:c.*3169A>G, NM_001286272.2:c.*3259A>G, NM_001286272.1:c.*3259A>G, NM_001286273.2:c.*3169A>G, NM_001286273.1:c.*3169A>G

Select item 14905515263.

rs1490551526 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 13:45333176 (GRCh38)
13:45907311 (GRCh37)
Canonical SPDI:: NC_000013.11:45333175:T:C
Gene:: TPT1 (Varview)
Functional Consequence:: 500B_downstream_variant,downstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000023/6 (TOPMED)
C=0.000039/5 (GnomAD)
HGVS:: NC_000013.11:g.45333176T>C, NC_000013.10:g.45907311T>C

Select item 14905195374.

rs1490519537 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: 13:45340027 (GRCh38)
13:45914162 (GRCh37)
Canonical SPDI:: NC_000013.11:45340026:G:A,NC_000013.11:45340026:G:C
Gene:: TPT1 (Varview), TPT1-AS1 (Varview), LOC124903169 (Varview)
Functional Consequence:: coding_sequence_variant,2KB_upstream_variant,upstream_transcript_variant,missense_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.000028/1 (ALFA)
C=0.000004/1 (GnomAD_exomes)
A=0.000004/1 (TOPMED)
A=0.000007/1 (GnomAD)
HGVS:: NC_000013.11:g.45340027G>A, NC_000013.11:g.45340027G>C, NC_000013.10:g.45914162G>A, NC_000013.10:g.45914162G>C, NM_003295.4:c.260C>T, NM_003295.4:c.260C>G, NM_003295.3:c.260C>T, NM_003295.3:c.260C>G, NM_003295.2:c.260C>T, NM_003295.2:c.260C>G, NM_001286272.2:c.260C>T, NM_001286272.2:c.260C>G, NM_001286272.1:c.260C>T, NM_001286272.1:c.260C>G, NM_001286273.2:c.158C>T, NM_001286273.2:c.158C>G, NM_001286273.1:c.158C>T, NM_001286273.1:c.158C>G, NP_003286.1:p.Ala87Val, NP_003286.1:p.Ala87Gly, NP_001273201.1:p.Ala87Val, NP_001273201.1:p.Ala87Gly, NP_001273202.1:p.Ala53Val, NP_001273202.1:p.Ala53Gly

Select item 14904382805.

rs1490438280 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 13:45333812 (GRCh38)
13:45907947 (GRCh37)
Canonical SPDI:: NC_000013.11:45333811:C:T
Gene:: TPT1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000007/1 (GnomAD)
T=0.000011/3 (TOPMED)
HGVS:: NC_000013.11:g.45333812C>T, NC_000013.10:g.45907947C>T, NM_003295.4:c.*3574G>A, NM_003295.3:c.*3574G>A, NM_001286272.2:c.*3664G>A, NM_001286272.1:c.*3664G>A, NM_001286273.2:c.*3574G>A, NM_001286273.1:c.*3574G>A

Select item 14901591716.

rs1490159171 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 13:45337387 (GRCh38)
13:45911522 (GRCh37)
Canonical SPDI:: NC_000013.11:45337386:T:C
Gene:: TPT1 (Varview), SNORA31 (Varview), SNORA31B (Varview)
Functional Consequence:: terminator_codon_variant,3_prime_UTR_variant,synonymous_variant,downstream_transcript_variant,upstream_transcript_variant,500B_downstream_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000004/1 (GnomAD_exomes)
C=0.000008/2 (TOPMED)
C=0.000014/2 (GnomAD)
HGVS:: NC_000013.11:g.45337387T>C, NC_000013.10:g.45911522T>C, NM_003295.4:c.518A>G, NM_003295.3:c.518A>G, NM_003295.2:c.518A>G, NM_001286272.2:c.*89A>G, NM_001286272.1:c.*89A>G, NM_001286273.2:c.416A>G, NM_001286273.1:c.416A>G

Select item 14901277357.

rs1490127735 [Homo sapiens]

Variant type:: DELINS
Alleles:: AA>-,A [Show Flanks]
Chromosome:: 13:45335424 (GRCh38)
13:45909559 (GRCh37)
Canonical SPDI:: NC_000013.11:45335422:AAA:A,NC_000013.11:45335422:AAA:AA
Gene:: TPT1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
-=0.000036/5 (GnomAD)
HGVS:: NC_000013.11:g.45335424_45335425del, NC_000013.11:g.45335425del, NC_000013.10:g.45909559_45909560del, NC_000013.10:g.45909560del, NM_003295.4:c.*1962_*1963del, NM_003295.4:c.*1963del, NM_003295.3:c.*1962_*1963del, NM_003295.3:c.*1963del, NM_001286272.2:c.*2052_*2053del, NM_001286272.2:c.*2053del, NM_001286272.1:c.*2052_*2053del, NM_001286272.1:c.*2053del, NM_001286273.2:c.*1962_*1963del, NM_001286273.2:c.*1963del, NM_001286273.1:c.*1962_*1963del, NM_001286273.1:c.*1963del

Select item 14901121558.

rs1490112155 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 13:45334597 (GRCh38)
13:45908732 (GRCh37)
Canonical SPDI:: NC_000013.11:45334596:C:T
Gene:: TPT1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000013.11:g.45334597C>T, NC_000013.10:g.45908732C>T, NM_003295.4:c.*2789G>A, NM_003295.3:c.*2789G>A, NM_001286272.2:c.*2879G>A, NM_001286272.1:c.*2879G>A, NM_001286273.2:c.*2789G>A, NM_001286273.1:c.*2789G>A

Select item 14899961039.

rs1489996103 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: 13:45340892 (GRCh38)
13:45915027 (GRCh37)
Canonical SPDI:: NC_000013.11:45340891:G:C
Gene:: TPT1 (Varview), TPT1-AS1 (Varview), LOC124903169 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000007/1 (GnomAD)
C=0.000011/3 (TOPMED)
HGVS:: NC_000013.11:g.45340892G>C, NC_000013.10:g.45915027G>C

Select item 148976144910.

rs1489761449 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 13:45343009 (GRCh38)
13:45917144 (GRCh37)
Canonical SPDI:: NC_000013.11:45343008:G:A
Gene:: TPT1 (Varview), TPT1-AS1 (Varview), LOC124903169 (Varview)
Functional Consequence:: intron_variant,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_000013.11:g.45343009G>A, NC_000013.10:g.45917144G>A

Select item 148882763911.

rs1488827639 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 13:45335785 (GRCh38)
13:45909920 (GRCh37)
Canonical SPDI:: NC_000013.11:45335784:A:G
Gene:: TPT1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000011/3 (TOPMED)
HGVS:: NC_000013.11:g.45335785A>G, NC_000013.10:g.45909920A>G, NM_003295.4:c.*1601T>C, NM_003295.3:c.*1601T>C, NM_001286272.2:c.*1691T>C, NM_001286272.1:c.*1691T>C, NM_001286273.2:c.*1601T>C, NM_001286273.1:c.*1601T>C

Select item 148879803012.

rs1488798030 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 13:45335060 (GRCh38)
13:45909195 (GRCh37)
Canonical SPDI:: NC_000013.11:45335059:G:A
Gene:: TPT1 (Varview)
Functional Consequence:: 3_prime_UTR_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_000013.11:g.45335060G>A, NC_000013.10:g.45909195G>A, NM_003295.4:c.*2326C>T, NM_003295.3:c.*2326C>T, NM_001286272.2:c.*2416C>T, NM_001286272.1:c.*2416C>T, NM_001286273.2:c.*2326C>T, NM_001286273.1:c.*2326C>T

Select item 148803135413.

rs1488031354 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 13:45341706 (GRCh38)
13:45915841 (GRCh37)
Canonical SPDI:: NC_000013.11:45341705:G:A
Gene:: TPT1 (Varview), TPT1-AS1 (Varview), LOC124903169 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by cluster
HGVS:: NC_000013.11:g.45341706G>A, NC_000013.10:g.45915841G>A

Select item 148801582314.

rs1488015823 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 13:45336834 (GRCh38)
13:45910969 (GRCh37)
Canonical SPDI:: NC_000013.11:45336833:G:A
Gene:: TPT1 (Varview), SNORA31B (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0./0 (GnomAD)
A=0.000019/5 (TOPMED)
HGVS:: NC_000013.11:g.45336834G>A, NC_000013.10:g.45910969G>A, NM_003295.4:c.*552C>T, NM_003295.3:c.*552C>T, NM_001286272.2:c.*642C>T, NM_001286272.1:c.*642C>T, NM_001286273.2:c.*552C>T, NM_001286273.1:c.*552C>T

Select item 148795294915.

rs1487952949 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,T [Show Flanks]
Chromosome:: 13:45341126 (GRCh38)
13:45915261 (GRCh37)
Canonical SPDI:: NC_000013.11:45341125:G:A,NC_000013.11:45341125:G:T
Gene:: TPT1 (Varview), TPT1-AS1 (Varview), LOC124903169 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
A=0.000011/3 (TOPMED)
HGVS:: NC_000013.11:g.45341126G>A, NC_000013.11:g.45341126G>T, NC_000013.10:g.45915261G>A, NC_000013.10:g.45915261G>T, NM_003295.4:c.-57C>T, NM_003295.4:c.-57C>A, NM_003295.3:c.-57C>T, NM_003295.3:c.-57C>A, NM_003295.2:c.-57C>T, NM_003295.2:c.-57C>A, NM_001286272.2:c.-57C>T, NM_001286272.2:c.-57C>A, NM_001286272.1:c.-57C>T, NM_001286272.1:c.-57C>A, NM_001286273.2:c.-85C>T, NM_001286273.2:c.-85C>A, NM_001286273.1:c.-85C>T, NM_001286273.1:c.-85C>A

Select item 148739253516.

rs1487392535 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->G [Show Flanks]
Chromosome:: 13:45337985 (GRCh38)
13:45912121 (GRCh37)
Canonical SPDI:: NC_000013.11:45337985:G:GG
Gene:: TPT1 (Varview), SNORA31 (Varview), SNORA31B (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: GG=0./0 (ALFA)
G=0.000026/7 (TOPMED)
G=0.000029/4 (GnomAD)
HGVS:: NC_000013.11:g.45337986dup, NC_000013.10:g.45912121dup

Select item 148720254117.

rs1487202541 [Homo sapiens]

Variant type:: DEL
Alleles:: CATATCCT>- [Show Flanks]
Chromosome:: 13:45334592 (GRCh38)
13:45908727 (GRCh37)
Canonical SPDI:: NC_000013.11:45334591:CATATCCT:
Gene:: TPT1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by cluster
MAF:: -=0.000021/3 (GnomAD)
-=0.000156/1 (1000Genomes)
HGVS:: NC_000013.11:g.45334592_45334599del, NC_000013.10:g.45908727_45908734del, NM_003295.4:c.*2787_*2794del, NM_003295.3:c.*2787_*2794del, NM_001286272.2:c.*2877_*2884del, NM_001286272.1:c.*2877_*2884del, NM_001286273.2:c.*2787_*2794del, NM_001286273.1:c.*2787_*2794del

Select item 148716195018.

rs1487161950 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 13:45335361 (GRCh38)
13:45909496 (GRCh37)
Canonical SPDI:: NC_000013.11:45335360:G:A
Gene:: TPT1 (Varview)
Functional Consequence:: 3_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000042/11 (TOPMED)
A=0.000156/1 (1000Genomes)
A=0.000248/4 (TOMMO)
A=0.000546/1 (Korea1K)
A=0.000684/2 (KOREAN)
HGVS:: NC_000013.11:g.45335361G>A, NC_000013.10:g.45909496G>A, NM_003295.4:c.*2025C>T, NM_003295.3:c.*2025C>T, NM_001286272.2:c.*2115C>T, NM_001286272.1:c.*2115C>T, NM_001286273.2:c.*2025C>T, NM_001286273.1:c.*2025C>T

Select item 148654083619.

rs1486540836 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 13:45336501 (GRCh38)
13:45910636 (GRCh37)
Canonical SPDI:: NC_000013.11:45336500:C:T
Gene:: TPT1 (Varview), SNORA31B (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,3_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.00003/8 (TOPMED)
HGVS:: NC_000013.11:g.45336501C>T, NC_000013.10:g.45910636C>T, NM_003295.4:c.*885G>A, NM_003295.3:c.*885G>A, NM_001286272.2:c.*975G>A, NM_001286272.1:c.*975G>A, NM_001286273.2:c.*885G>A, NM_001286273.1:c.*885G>A

Select item 148634307020.

rs1486343070 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,T [Show Flanks]
Chromosome:: 13:45339675 (GRCh38)
13:45913810 (GRCh37)
Canonical SPDI:: NC_000013.11:45339674:C:A,NC_000013.11:45339674:C:T
Gene:: TPT1 (Varview), TPT1-AS1 (Varview), LOC124903169 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000007/1 (GnomAD)
A=0.000035/1 (TOMMO)
HGVS:: NC_000013.11:g.45339675C>A, NC_000013.11:g.45339675C>T, NC_000013.10:g.45913810C>A, NC_000013.10:g.45913810C>T

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