chr2:214986579:A>G Detail (hg38) (ABCA12)

Information

Genome

Assembly Position
hg19 chr2:215,851,303-215,851,303 View the variant detail on this assembly version.
hg38 chr2:214,986,579-214,986,579

HGVS

Type Transcript Protein
RefSeq NM_173076.2:c.4126T>C NP_775099.2:p.Leu1376=
NR_103740.1:c.4126T>C
NM_015657.3:c.3172T>C NP_056472.2:p.Leu1058=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.046
ToMMo:0.067
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.040

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 607800 OMIM
HGNC 14637 HGNC
Ensembl ENSG00000144452 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv10445516 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign criteria provided, single submitter not specified germline Detail
Benign 2018-01-13 criteria provided, single submitter Congenital ichthyosis of skin germline Detail
Benign 2021-07-14 criteria provided, single submitter autosomal recessive congenital ichthyosis 4A germline Detail
Benign 2021-07-14 criteria provided, single submitter autosomal recessive congenital ichthyosis 4B germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_173076.3(ABCA12):c.4126T>C (p.Leu1376=) AND not specified ClinVar Detail
NM_173076.3(ABCA12):c.4126T>C (p.Leu1376=) AND Congenital ichthyosis of skin ClinVar Detail
NM_173076.3(ABCA12):c.4126T>C (p.Leu1376=) AND Autosomal recessive congenital ichthyosis 4A ClinVar Detail
NM_173076.3(ABCA12):c.4126T>C (p.Leu1376=) AND Autosomal recessive congenital ichthyosis 4B ClinVar Detail
NM_173076.3(ABCA12):c.4126T>C (p.Leu1376=) AND not provided 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
rs34351934 dbSNP
Genome
hg38
Position
chr2:214,986,579-214,986,579
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1079
Mean of sample read depth (HGVD)
26.68
Standard deviation of sample read depth (HGVD)
16.14
Number of reference allele (HGVD)
2058
Number of alternative allele (HGVD)
100
Allele Frequency (HGVD)
0.04633920296570899
Gene Symbol (HGVD)
ABCA12
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))
rs34351934
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0666
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1116
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8624
East Asian Allele Counts (ExAC)
347
East Asian Heterozygous Counts (ExAC)
333
East Asian Homozygous Counts (ExAC)
7
East Asian Allele Frequency (ExAC)
0.040236549165120594
Chromosome Counts in All Race (ExAC)
121274
Allele Counts in All Race (ExAC)
16440
Heterozygous Counts in All Race (ExAC)
13034
Homozygous Counts in All Race (ExAC)
1703
Allele Frequency in All Race (ExAC)
0.13556079621353298
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