chr2:203867624:C>T Detail (hg38) (CTLA4)

Information

Genome

Assembly Position
hg19 chr2:204,732,347-204,732,347 View the variant detail on this assembly version.
hg38 chr2:203,867,624-203,867,624

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000696479.1:c.48-294C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.107
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 123890 OMIM
HGNC 2505 HGNC
Ensembl ENSG00000163599 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv10206412 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2023-12-19 criteria provided, single submitter Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsuffiency germline Detail
Benign 2018-11-11 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Metabolic syndrome X In a marker-by-marker analysis, the ADRB2 rs180088 (OR 1.22, 95% CI 1.01-1.48) a... BeFree 19619703 Detail
0.064 Autoimmune Diseases Six autoimmune disease-related risk alleles of CTLA4 (rs1863800, rs733618, rs455... BeFree 25003519 Detail
0.002 osteosarcoma The current study evaluated the association of four CTLA-4 gene mutations, -1661... BeFree 21612409 Detail
0.001 Osteosarcoma of bone The current study evaluated the association of four CTLA-4 gene mutations, -1661... BeFree 21612409 Detail
0.010 cervix carcinoma Association of CTLA4 gene polymorphism (rs5742909) with cervical cancer: a meta-... BeFree 24122201 Detail
0.003 Malignant tumor of cervix Association of CTLA4 gene polymorphism (rs5742909) with cervical cancer: a meta-... BeFree 24122201 Detail
Annotation

Annotations

DescrptionSourceLinks
NC_000002.12:g.203867624C>T AND Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsuffienc... ClinVar Detail
NC_000002.12:g.203867624C>T AND not provided ClinVar Detail
In a marker-by-marker analysis, the ADRB2 rs180088 (OR 1.22, 95% CI 1.01-1.48) and PAI1 rs1799768 (O... DisGeNET Detail
Six autoimmune disease-related risk alleles of CTLA4 (rs1863800, rs733618, rs4553808, rs5742909, rs2... DisGeNET Detail
The current study evaluated the association of four CTLA-4 gene mutations, -1661A/G (rs4553808), -31... DisGeNET Detail
The current study evaluated the association of four CTLA-4 gene mutations, -1661A/G (rs4553808), -31... DisGeNET Detail
Association of CTLA4 gene polymorphism (rs5742909) with cervical cancer: a meta-analysis. DisGeNET Detail
Association of CTLA4 gene polymorphism (rs5742909) with cervical cancer: a meta-analysis. DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs5742909 dbSNP
Genome
hg38
Position
chr2:203,867,624-203,867,624
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))
rs5742909
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1074
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1800
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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