chr4:100512392:G>A Detail (hg19) (MTTP)

Information

Genome

Assembly Position
hg19 chr4:100,512,392-100,512,392
hg38 chr4:99,591,235-99,591,235 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000253.3:c.502G>A NP_000244.2:p.Val168Ile
NM_001300785.1:c.253G>A NP_001287714.1:p.Val85Ile
Ensemble ENST00000265517.10:c.502G>A ENST00000265517.10:p.Val168Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.009
ToMMo:0.012
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.012

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 157147 OMIM
HGNC 7467 HGNC
Ensembl ENSG00000138823 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv18023405 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2021-05-18 criteria provided, multiple submitters, no conflicts Abetalipoproteinaemia germline Detail
Benign Likely benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign no assertion criteria provided not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.004 Hypobetalipoproteinemias MTP gene sequence revealed that he was a carrier of the I128T polymorphism and a... BeFree 14732481 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001386140.1(MTTP):c.502G>A (p.Val168Ile) AND Abetalipoproteinaemia ClinVar Detail
NM_001386140.1(MTTP):c.502G>A (p.Val168Ile) AND not provided ClinVar Detail
NM_001386140.1(MTTP):c.502G>A (p.Val168Ile) AND not specified ClinVar Detail
MTP gene sequence revealed that he was a carrier of the I128T polymorphism and an unreported amino a... 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
rs61750974 dbSNP
Genome
hg19
Position
chr4:100,512,392-100,512,392
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
108.03
Standard deviation of sample read depth (HGVD)
46.91
Number of reference allele (HGVD)
2398
Number of alternative allele (HGVD)
22
Allele Frequency (HGVD)
0.00909090909090909
Gene Symbol (HGVD)
MTTP
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))
rs61750974
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0121
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
203
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
102
East Asian Heterozygous Counts (ExAC)
100
East Asian Homozygous Counts (ExAC)
1
East Asian Allele Frequency (ExAC)
0.011791907514450866
Chromosome Counts in All Race (ExAC)
121390
Allele Counts in All Race (ExAC)
1236
Heterozygous Counts in All Race (ExAC)
1204
Homozygous Counts in All Race (ExAC)
16
Allele Frequency in All Race (ExAC)
0.010182057830134279
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