chr11:13492716:C>T Detail (hg38) (PTH)

Information

Genome

Assembly Position
hg19 chr11:13,514,263-13,514,263 View the variant detail on this assembly version.
hg38 chr11:13,492,716-13,492,716

HGVS

Type Transcript Protein
RefSeq NM_000315.3:c.87-50G>A
NM_001316352.1:c.87-50G>A
Ensemble ENST00000282091.6:c.87-50G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.092
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.115

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 168450 OMIM
HGNC 9606 HGNC
Ensembl ENSG00000152266 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv41682325 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-11-12 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 aortic valve stenosis Finally, rs1544410 polymorphism within the VDR gene, E2 and E4 alleles within th... BeFree 24903972 Detail
0.003 aortic valve stenosis Finally, rs1544410 polymorphism within the VDR gene, E2 and E4 alleles within th... BeFree 24903972 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000315.4(PTH):c.87-50G>A AND not provided ClinVar Detail
Finally, rs1544410 polymorphism within the VDR gene, E2 and E4 alleles within the apoE gene, rs6254 ... DisGeNET Detail
Finally, rs1544410 polymorphism within the VDR gene, E2 and E4 alleles within the apoE gene, rs6254 ... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs6254 dbSNP
Genome
hg38
Position
chr11:13,492,716-13,492,716
Variant Type
snv
Reference Allele
C
Alternative Allele
T
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs6254
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0917
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1536
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8570
East Asian Allele Counts (ExAC)
983
East Asian Heterozygous Counts (ExAC)
859
East Asian Homozygous Counts (ExAC)
62
East Asian Allele Frequency (ExAC)
0.1147024504084014
Chromosome Counts in All Race (ExAC)
120366
Allele Counts in All Race (ExAC)
34097
Heterozygous Counts in All Race (ExAC)
23155
Homozygous Counts in All Race (ExAC)
5471
Allele Frequency in All Race (ExAC)
0.2832776697738564
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