chr4:89883979:C>T Detail (hg19) (FAM13A)

Information

Genome

Assembly Position
hg19 chr4:89,883,979-89,883,979
hg38 chr4:88,962,828-88,962,828 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_014883.3:c.606-24587G>A
Ensemble ENST00000264344.10:c.606-24587G>A
ENST00000509094.5:c.606-24587G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.592
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 613299 OMIM
HGNC 19367 HGNC
Ensembl ENSG00000138640 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv17812302 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
association 2020-02-03 no assertion criteria provided chronic obstructive pulmonary disease germline Detail
Benign 2020-02-17 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 pulmonary emphysema The emphysema-predominant GOLD 1 cluster was nominally associated with rs7671167... BeFree 25154699 Detail
<0.001 pulmonary emphysema The emphysema-predominant GOLD 1 cluster was nominally associated with rs7671167... BeFree 25154699 Detail
0.248 Chronic Obstructive Airway Disease Variants in FAM13A are associated with chronic obstructive pulmonary disease. GWASCAT 20173748 Detail
0.248 Chronic Obstructive Airway Disease [Variants in FAM13A are associated with chronic obstructive pulmonary disease.] GAD 20173748 Detail
0.003 Chronic Obstructive Airway Disease We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13... BeFree 22461431 Detail
<0.001 Chronic Obstructive Airway Disease We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13... BeFree 22461431 Detail
0.248 Chronic Obstructive Airway Disease We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13... BeFree 22461431 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_014883.4(FAM13A):c.606-24587G>A AND Chronic obstructive pulmonary disease ClinVar Detail
NM_014883.4(FAM13A):c.606-24587G>A AND not provided ClinVar Detail
The emphysema-predominant GOLD 1 cluster was nominally associated with rs7671167 (FAM13A) and rs1619... DisGeNET Detail
The emphysema-predominant GOLD 1 cluster was nominally associated with rs7671167 (FAM13A) and rs1619... DisGeNET Detail
Variants in FAM13A are associated with chronic obstructive pulmonary disease. DisGeNET Detail
[Variants in FAM13A are associated with chronic obstructive pulmonary disease.] DisGeNET Detail
We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13180 (IREB2), and rs8... DisGeNET Detail
We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13180 (IREB2), and rs8... DisGeNET Detail
We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13180 (IREB2), and rs8... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs7671167 dbSNP
Genome
hg19
Position
chr4:89,883,979-89,883,979
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs7671167
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5923
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9927
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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