chr19:1058189:T>C Detail (hg38) (ABCA7)

Information

Genome

Assembly Position
hg19 chr19:1,058,188-1,058,188 View the variant detail on this assembly version.
hg38 chr19:1,058,189-1,058,189

HGVS

Type Transcript Protein
RefSeq NM_019112.3:c.5069T>C NP_061985.2:p.Ile1690Thr
Ensemble ENST00000263094.11:c.5069T>C ENST00000263094.11:p.Ile1690Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.017
ToMMo:0.018
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.004

Prediction

ClinVar

Clinical Significance Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 605414 OMIM
HGNC 37 HGNC
Ensembl ENSG00000064687 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv60735744 TogoVar
COSMIC COSM3680769 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely benign 2022-04-01 criteria provided, single submitter not provided germline Detail
Likely benign 2019-06-13 criteria provided, single submitter ABCA7-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_019112.4(ABCA7):c.5069T>C (p.Ile1690Thr) AND not provided ClinVar Detail
NM_019112.4(ABCA7):c.5069T>C (p.Ile1690Thr) AND ABCA7-related disorder ClinVar 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
rs184218896 dbSNP
Genome
hg38
Position
chr19:1,058,189-1,058,189
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1208
Mean of sample read depth (HGVD)
117.15
Standard deviation of sample read depth (HGVD)
54.94
Number of reference allele (HGVD)
2375
Number of alternative allele (HGVD)
41
Allele Frequency (HGVD)
0.01697019867549669
Gene Symbol (HGVD)
ABCA7
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))
rs184218896
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0178
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
298
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8640
East Asian Allele Counts (ExAC)
36
East Asian Heterozygous Counts (ExAC)
32
East Asian Homozygous Counts (ExAC)
2
East Asian Allele Frequency (ExAC)
0.004166666666666667
Chromosome Counts in All Race (ExAC)
120852
Allele Counts in All Race (ExAC)
36
Heterozygous Counts in All Race (ExAC)
32
Homozygous Counts in All Race (ExAC)
2
Allele Frequency in All Race (ExAC)
2.978850163836759E-4
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