chr7:37947103:C>T Detail (hg19) (SFRP4)

Information

Genome

Assembly Position
hg19 chr7:37,947,103-37,947,103
hg38 chr7:37,907,501-37,907,501 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_003014.3:c.1019G>A NP_003005.2:p.Arg340Lys
Ensemble ENST00000436072.7:c.1019G>A ENST00000436072.7:p.Arg340Lys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.226
ToMMo:0.232
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.244

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606570 OMIM
HGNC 10778 HGNC
Ensembl ENSG00000106483 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv28955524 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-07-15 criteria provided, single submitter Pyle metaphyseal dysplasia germline Detail
Benign 2024-01-31 criteria provided, single submitter not provided germline Detail
Benign 2019-10-21 criteria provided, single submitter SFRP4-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 renal cell carcinoma including Dickkopf 2 (DKK2) (reference SNP identification number 17037102 [rs170... BeFree 19562778 Detail
0.003 renal cell carcinoma including Dickkopf 2 (DKK2) (reference SNP identification number 17037102 [rs170... BeFree 19562778 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003014.4(SFRP4):c.1019G>A (p.Arg340Lys) AND Pyle metaphyseal dysplasia ClinVar Detail
NM_003014.4(SFRP4):c.1019G>A (p.Arg340Lys) AND not provided ClinVar Detail
NM_003014.4(SFRP4):c.1019G>A (p.Arg340Lys) AND SFRP4-related disorder ClinVar Detail
including Dickkopf 2 (DKK2) (reference SNP identification number 17037102 [rs17037102], rs419558, an... DisGeNET Detail
including Dickkopf 2 (DKK2) (reference SNP identification number 17037102 [rs17037102], rs419558, an... 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
rs1802074 dbSNP
Genome
hg19
Position
chr7:37,947,103-37,947,103
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1150
Mean of sample read depth (HGVD)
46.54
Standard deviation of sample read depth (HGVD)
28.51
Number of reference allele (HGVD)
1781
Number of alternative allele (HGVD)
519
Allele Frequency (HGVD)
0.22565217391304349
Gene Symbol (HGVD)
SFRP4
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))
rs1802074
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2324
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3894
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8644
East Asian Allele Counts (ExAC)
2110
East Asian Heterozygous Counts (ExAC)
1608
East Asian Homozygous Counts (ExAC)
251
East Asian Allele Frequency (ExAC)
0.24409995372512724
Chromosome Counts in All Race (ExAC)
121054
Allele Counts in All Race (ExAC)
24591
Heterozygous Counts in All Race (ExAC)
19001
Homozygous Counts in All Race (ExAC)
2795
Allele Frequency in All Race (ExAC)
0.20314074710459795
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