chr19:7619760:A>C Detail (hg19) (PNPLA6)

Information

Genome

Assembly Position
hg19 chr19:7,619,760-7,619,760
hg38 chr19:7,554,874-7,554,874 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_006702.4:c.2521-19A>C
NM_001166111.1:c.2665-19A>C
NM_001166113.1:c.2521-19A>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.286
ToMMo:0.308
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.308

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 603197 OMIM
HGNC 16268 HGNC
Ensembl ENSG00000032444 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv61038470 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-01-22 criteria provided, single submitter not specified germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts hereditary spastic paraplegia 39 germline Detail
Benign 2021-10-25 criteria provided, single submitter Ataxia-hypogonadism-choroidal dystrophy syndrome germline Detail
Benign 2021-10-25 criteria provided, single submitter Trichomegaly-retina pigmentary degeneration-dwarfism syndrome germline Detail
Benign 2021-10-25 criteria provided, single submitter Laurence-Moon syndrome germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_001166114.2(PNPLA6):c.2635-19A>C AND not specified ClinVar Detail
NM_001166114.2(PNPLA6):c.2635-19A>C AND Hereditary spastic paraplegia 39 ClinVar Detail
NM_001166114.2(PNPLA6):c.2635-19A>C AND Ataxia-hypogonadism-choroidal dystrophy syndrome ClinVar Detail
NM_001166114.2(PNPLA6):c.2635-19A>C AND Trichomegaly-retina pigmentary degeneration-dwarfism syndrom... ClinVar Detail
NM_001166114.2(PNPLA6):c.2635-19A>C AND Laurence-Moon syndrome ClinVar Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs539887 dbSNP
Genome
hg19
Position
chr19:7,619,760-7,619,760
Variant Type
snv
Reference Allele
A
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
807
Mean of sample read depth (HGVD)
81.61
Standard deviation of sample read depth (HGVD)
38.27
Number of reference allele (HGVD)
1152
Number of alternative allele (HGVD)
462
Allele Frequency (HGVD)
0.2862453531598513
Gene Symbol (HGVD)
PNPLA6
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))
rs539887
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3083
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5163
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16748
East Asian Chromosome Counts (ExAC)
4834
East Asian Allele Counts (ExAC)
1488
East Asian Heterozygous Counts (ExAC)
1132
East Asian Homozygous Counts (ExAC)
178
East Asian Allele Frequency (ExAC)
0.3078196110881258
Chromosome Counts in All Race (ExAC)
69282
Allele Counts in All Race (ExAC)
25551
Heterozygous Counts in All Race (ExAC)
17315
Homozygous Counts in All Race (ExAC)
4118
Allele Frequency in All Race (ExAC)
0.36879709015328654
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