SNP Links for Gene (Select 7258) - SNP

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: Y:9466078 (GRCh38)
Y:9303687 (GRCh37)
Canonical SPDI:: NC_000024.10:9466077:C:T
Gene:: TSPY1 (Varview), FAM197Y5 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
HGVS:: NC_000024.10:g.9466078C>T, NC_000024.9:g.9303687C>T, NG_027958.1:g.4124C>T, NW_025791821.1:g.690846C>T

Select item 14648467236.

rs1464846723 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: Y:9467327 (GRCh38)
Y:9304936 (GRCh37)
Canonical SPDI:: NC_000024.10:9467326:G:A
Gene:: TSPY1 (Varview)
Functional Consequence:: intron_variant,coding_sequence_variant,non_coding_transcript_variant,synonymous_variant
HGVS:: NC_000024.10:g.9467327G>A, NC_000024.9:g.9304936G>A, NG_027958.1:g.5373G>A, NM_003308.4:c.327G>A, NM_003308.3:c.327G>A, NM_001197242.2:c.327G>A, NM_001197242.1:c.327G>A, NW_025791821.1:g.692113G>A, XR_001756005.2:n.373G>A, XR_001756005.1:n.348G>A, XM_017030064.2:c.327G>A, XM_017030064.1:c.327G>A, NM_001282469.1:c.327G>A, NM_001282469.3:c.327G>A, NM_001282469.2:c.327G>A

Select item 14576320457.

rs1457632045 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: Y:9468869 (GRCh38)
Y:9306478 (GRCh37)
Canonical SPDI:: NC_000024.10:9468868:A:G
Gene:: TSPY1 (Varview)
Functional Consequence:: intron_variant
HGVS:: NC_000024.10:g.9468869A>G, NC_000024.9:g.9306478A>G, NG_027958.1:g.6915A>G, NW_025791821.1:g.693655A>G

Select item 14563243148.

rs1456324314 [Homo sapiens]

Variant type:: INS
Alleles:: ->TGTCT [Show Flanks]
Chromosome:: Y:9466068 (GRCh38)
Y:9303678 (GRCh37)
Canonical SPDI:: NC_000024.10:9466068::TGTCT
Gene:: TSPY1 (Varview), FAM197Y5 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: -=0./0 (ALFA)
HGVS:: NC_000024.10:g.9466068_9466069insTGTCT, NC_000024.9:g.9303677_9303678insTGTCT, NG_027958.1:g.4114_4115insTGTCT, NW_025791821.1:g.690834_690835insTGTCT

Select item 14552236359.

rs1455223635 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->AG [Show Flanks]
Chromosome:: Y:9468993 (GRCh38)
Y:9306603 (GRCh37)
Canonical SPDI:: NC_000024.10:9468993:AGAG:AGAGAG
Gene:: TSPY1 (Varview)
Functional Consequence:: intron_variant
HGVS:: NC_000024.10:g.9468994AG[3], NC_000024.9:g.9306603AG[3], NG_027958.1:g.7040AG[3], NW_025791821.1:g.693780AG[4]

Select item 145421380310.

rs1454213803 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: Y:9469430 (GRCh38)
Y:9307039 (GRCh37)
Canonical SPDI:: NC_000024.10:9469429:G:A
Gene:: TSPY1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency,by cluster
MAF:: A=0.0589/65 (KOREAN)
G=0.25/1 (SGDP_PRJ)
HGVS:: NC_000024.10:g.9469430G>A, NC_000024.9:g.9307039G>A, NG_027958.1:g.7476G>A, NW_025791821.1:g.694218G>A

Select item 145346576311.

rs1453465763 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: Y:9468575 (GRCh38)
Y:9306184 (GRCh37)
Canonical SPDI:: NC_000024.10:9468574:C:T
Gene:: TSPY1 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant,non_coding_transcript_variant,synonymous_variant
Validated:: by frequency,by cluster
MAF:: T=0.00008/1 (GnomAD_exomes)
C=0.5/1 (SGDP_PRJ)
HGVS:: NC_000024.10:g.9468575C>T, NC_000024.9:g.9306184C>T, NG_027958.1:g.6621C>T, NM_003308.4:c.739C>T, NM_003308.3:c.739C>T, NM_001197242.2:c.739C>T, NM_001197242.1:c.739C>T, NM_001320964.2:c.478C>T, NM_001320964.1:c.478C>T, NW_025791821.1:g.693361C>T, XR_001756005.2:n.778C>T, XR_001756005.1:n.753C>T, XM_017030064.2:c.732C>T, XM_017030064.1:c.732C>T, NM_001282469.1:c.739C>T, NM_001282469.3:c.739C>T, NM_001282469.2:c.739C>T, NP_003299.2:p.Arg247Cys, NP_001184171.1:p.Arg247Cys, NP_001307893.1:p.Arg160Cys

Select item 145213722512.

rs1452137225 [Homo sapiens]

Variant type:: DEL
Alleles:: A>- [Show Flanks]
Chromosome:: Y:9466836 (GRCh38)
Y:9304445 (GRCh37)
Canonical SPDI:: NC_000024.10:9466835:A:
Gene:: TSPY1 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
HGVS:: NC_000024.10:g.9466836del, NC_000024.9:g.9304445del, NG_027958.1:g.4882del

Select item 145069430713.

rs1450694307 [Homo sapiens]

Variant type:: SNV
Alleles:: C>G,T [Show Flanks]
Chromosome:: Y:9466129 (GRCh38)
Y:9303738 (GRCh37)
Canonical SPDI:: NC_000024.10:9466128:C:G,NC_000024.10:9466128:C:T
Gene:: TSPY1 (Varview), FAM197Y5 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
HGVS:: NC_000024.10:g.9466129C>G, NC_000024.10:g.9466129C>T, NC_000024.9:g.9303738C>G, NC_000024.9:g.9303738C>T, NG_027958.1:g.4175C>G, NG_027958.1:g.4175C>T, NW_025791821.1:g.690897G>C, NW_025791821.1:g.690897G>T

Select item 143988260014.

rs1439882600 has merged into rs878985284 [Homo sapiens]

Variant type:: DELINS
Alleles:: GTGTGTGT>-,GTGT,GTGTGT,GTGTGTGTGT,GTGTGTGTGTGT,GTGTGTGTGTGTGT [Show Flanks]
Chromosome:: Y:9469813 (GRCh38)
Y:9307422 (GRCh37)
Canonical SPDI:: NC_000024.10:9469789:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGTGTGTGT,NC_000024.10:9469789:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGTGTGTGTGTGT,NC_000024.10:9469789:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGTGTGTGTGTGTGT,NC_000024.10:9469789:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT,NC_000024.10:9469789:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT,NC_000024.10:9469789:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT:TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
Gene:: TSPY1 (Varview)
Functional Consequence:: 500B_downstream_variant,downstream_transcript_variant
Validated:: by cluster
HGVS:: NC_000024.10:g.9469791GT[11], NC_000024.10:g.9469791GT[13], NC_000024.10:g.9469791GT[14], NC_000024.10:g.9469791GT[16], NC_000024.10:g.9469791GT[17], NC_000024.10:g.9469791GT[18], NC_000024.9:g.9307400GT[11], NC_000024.9:g.9307400GT[13], NC_000024.9:g.9307400GT[14], NC_000024.9:g.9307400GT[16], NC_000024.9:g.9307400GT[17], NC_000024.9:g.9307400GT[18], NG_027958.1:g.7837GT[11], NG_027958.1:g.7837GT[13], NG_027958.1:g.7837GT[14], NG_027958.1:g.7837GT[16], NG_027958.1:g.7837GT[17], NG_027958.1:g.7837GT[18], NW_025791821.1:g.694579_694593delinsGTGTGTGTGTGTGTGTG, NW_025791821.1:g.694579_694593delinsGTGTGTGTG, NW_025791821.1:g.694579_694593delinsGTGTGTGTGTGTG, NW_025791821.1:g.694579_694593delinsGTGTGTGTGTGTGTG, NW_025791821.1:g.694579_694593delinsGTGTGTGTGTGTGTGTGTG, NW_025791821.1:g.694579_694593delinsGTGTGTGTGTGTGTGTGTGTG, NW_025791821.1:g.694579_694593delinsGTGTGTGTGTGTGTGTGTGTGTG

Select item 143946041815.

rs1439460418 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: Y:9468700 (GRCh38)
Y:9306309 (GRCh37)
Canonical SPDI:: NC_000024.10:9468699:T:A
Gene:: TSPY1 (Varview)
Functional Consequence:: intron_variant
Validated:: by frequency
MAF:: A=0.00007/1 (GnomAD_exomes)
HGVS:: NC_000024.10:g.9468700T>A, NC_000024.9:g.9306309T>A, NG_027958.1:g.6746T>A, NW_025791821.1:g.693486T>A

Select item 143602646216.

rs1436026462 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: Y:9466924 (GRCh38)
Y:9304533 (GRCh37)
Canonical SPDI:: NC_000024.10:9466923:C:T
Gene:: TSPY1 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
HGVS:: NC_000024.10:g.9466924C>T, NC_000024.9:g.9304533C>T, NG_027958.1:g.4970C>T, NW_025791821.1:g.691692C>T

Select item 143183785617.

rs1431837856 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: Y:9467451 (GRCh38)
Y:9305060 (GRCh37)
Canonical SPDI:: NC_000024.10:9467450:G:C
Gene:: TSPY1 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.0005/1 (ALFA)
C=0.0038/5 (KOREAN)
HGVS:: NC_000024.10:g.9467451G>C, NC_000024.9:g.9305060G>C, NG_027958.1:g.5497G>C, NM_003308.4:c.451G>C, NM_003308.3:c.451G>C, NM_001197242.2:c.451G>C, NM_001197242.1:c.451G>C, NM_001320964.2:c.190G>C, NM_001320964.1:c.190G>C, NW_025791821.1:g.692237G>C, XR_001756005.2:n.497G>C, XR_001756005.1:n.472G>C, XM_017030064.2:c.451G>C, XM_017030064.1:c.451G>C, NM_001282469.1:c.451G>C, NM_001282469.3:c.451G>C, NM_001282469.2:c.451G>C, NP_003299.2:p.Val151Leu, NP_001184171.1:p.Val151Leu, NP_001307893.1:p.Val64Leu, XP_016885553.1:p.Val151Leu

Select item 142579899118.

rs1425798991 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: Y:9466076 (GRCh38)
Y:9303685 (GRCh37)
Canonical SPDI:: NC_000024.10:9466075:C:T
Gene:: TSPY1 (Varview), FAM197Y5 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
HGVS:: NC_000024.10:g.9466076C>T, NC_000024.9:g.9303685C>T, NG_027958.1:g.4122C>T, NW_025791821.1:g.690844C>T

Select item 142313653119.

rs1423136531 [Homo sapiens]

Variant type:: INS
Alleles:: ->GGA [Show Flanks]
Chromosome:: Y:9466072 (GRCh38)
Y:9303682 (GRCh37)
Canonical SPDI:: NC_000024.10:9466072::GGA
Gene:: TSPY1 (Varview), FAM197Y5 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
HGVS:: NC_000024.10:g.9466072_9466073insGGA, NC_000024.9:g.9303681_9303682insGGA, NG_027958.1:g.4118_4119insGGA, NW_025791821.1:g.690840_690841insGGA

Select item 142178988420.

rs1421789884 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G,T [Show Flanks]
Chromosome:: Y:9467317 (GRCh38)
Y:9304926 (GRCh37)
Canonical SPDI:: NC_000024.10:9467316:A:G,NC_000024.10:9467316:A:T
Gene:: TSPY1 (Varview)
Functional Consequence:: missense_variant,intron_variant,coding_sequence_variant,non_coding_transcript_variant
Validated:: by frequency,by cluster
MAF:: G=0.00003/1 (GnomAD_exomes)
A=0.5/1 (SGDP_PRJ)
HGVS:: NC_000024.10:g.9467317A>G, NC_000024.10:g.9467317A>T, NC_000024.9:g.9304926A>G, NC_000024.9:g.9304926A>T, NG_027958.1:g.5363A>G, NG_027958.1:g.5363A>T, NM_003308.4:c.317A>G, NM_003308.4:c.317A>T, NM_003308.3:c.317A>G, NM_003308.3:c.317A>T, NM_001197242.2:c.317A>G, NM_001197242.2:c.317A>T, NM_001197242.1:c.317A>G, NM_001197242.1:c.317A>T, NW_025791821.1:g.692103A>G, NW_025791821.1:g.692103A>T, XR_001756005.2:n.363A>G, XR_001756005.2:n.363A>T, XR_001756005.1:n.338A>G, XR_001756005.1:n.338A>T, XM_017030064.2:c.317A>G, XM_017030064.2:c.317A>T, XM_017030064.1:c.317A>G, XM_017030064.1:c.317A>T, NM_001282469.1:c.317A>G, NM_001282469.1:c.317A>T, NM_001282469.3:c.317A>G, NM_001282469.3:c.317A>T, NM_001282469.2:c.317A>G, NM_001282469.2:c.317A>T, NP_003299.2:p.Glu106Gly, NP_003299.2:p.Glu106Val, NP_001184171.1:p.Glu106Gly, NP_001184171.1:p.Glu106Val, XP_016885553.1:p.Glu106Gly, XP_016885553.1:p.Glu106Val

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