chr17:12899902:C>T Detail (hg19) (ELAC2)

Information

Genome

Assembly Position
hg19 chr17:12,899,902-12,899,902
hg38 chr17:12,996,585-12,996,585 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001165962.1:c.1501G>A NP_001159434.1:p.Ala501Thr
NM_018127.6:c.1621G>A NP_060597.4:p.Ala541Thr
NM_173717.1:c.1621G>A NP_776065.1:p.Ala541Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.003
ToMMo:0.002
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.007

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 605367 OMIM
HGNC 14198 HGNC
Ensembl ENSG00000006744 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv57125587 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2002-12-01 no assertion criteria provided Prostate cancer, hereditary, 2 germline Detail
Benign 2016-03-29 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign Likely benign 2024-02-01 criteria provided, multiple submitters, no conflicts Combined oxidative phosphorylation defect type 17 germline unknown Detail
Benign 2016-02-15 no assertion criteria provided not provided unknown Detail
Likely benign 2021-10-26 criteria provided, single submitter Combined oxidative phosphorylation defect type 17,Prostate cancer, hereditary, 2 unknown Detail
Likely benign 2021-10-26 criteria provided, single submitter Combined oxidative phosphorylation defect type 17,Prostate cancer, hereditary, 2 unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.240 Prostate cancer, hereditary, 2 NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_018127.7(ELAC2):c.1621G>A (p.Ala541Thr) AND Prostate cancer, hereditary, 2 ClinVar Detail
NM_018127.7(ELAC2):c.1621G>A (p.Ala541Thr) AND not specified ClinVar Detail
NM_018127.7(ELAC2):c.1621G>A (p.Ala541Thr) AND Combined oxidative phosphorylation defect type 17 ClinVar Detail
NM_018127.7(ELAC2):c.1621G>A (p.Ala541Thr) AND not provided ClinVar Detail
NM_018127.7(ELAC2):c.1621G>A (p.Ala541Thr) AND multiple conditions ClinVar Detail
NM_018127.7(ELAC2):c.1621G>A (p.Ala541Thr) AND multiple conditions ClinVar Detail
NA DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs5030739 dbSNP
Genome
hg19
Position
chr17:12,899,902-12,899,902
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1183
Mean of sample read depth (HGVD)
37.00
Standard deviation of sample read depth (HGVD)
19.14
Number of reference allele (HGVD)
2358
Number of alternative allele (HGVD)
8
Allele Frequency (HGVD)
0.0033812341504649195
Gene Symbol (HGVD)
ELAC2
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))
rs5030739
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0023
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
39
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8582
East Asian Allele Counts (ExAC)
57
East Asian Heterozygous Counts (ExAC)
57
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.006641808436261944
Chromosome Counts in All Race (ExAC)
120648
Allele Counts in All Race (ExAC)
4151
Heterozygous Counts in All Race (ExAC)
3963
Homozygous Counts in All Race (ExAC)
94
Allele Frequency in All Race (ExAC)
0.034405874941979976
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