chr7:37907562:G>T Detail (hg38) (SFRP4)

Information

Genome

Assembly Position
hg19 chr7:37,947,164-37,947,164 View the variant detail on this assembly version.
hg38 chr7:37,907,562-37,907,562

HGVS

Type Transcript Protein
RefSeq NM_003014.3:c.958C>A NP_003005.2:p.Pro320Thr
Ensemble ENST00000436072.7:c.958C>A ENST00000436072.7:p.Pro320Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.484
ToMMo:0.496
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.548

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 tgv28955540 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2021-07-15 criteria provided, single submitter Pyle metaphyseal dysplasia germline Detail
Benign 2019-10-17 criteria provided, single submitter SFRP4-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 colorectal cancer In addition, homozygosity for the minor allele of SFRP4 P320T was significantly ... BeFree 20403915 Detail
<0.001 Rectal Carcinoma In addition, homozygosity for the minor allele of SFRP4 P320T was significantly ... BeFree 20403915 Detail
<0.001 colorectal carcinoma In addition, homozygosity for the minor allele of SFRP4 P320T was significantly ... BeFree 20403915 Detail
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.958C>A (p.Pro320Thr) AND not provided ClinVar Detail
NM_003014.4(SFRP4):c.958C>A (p.Pro320Thr) AND Pyle metaphyseal dysplasia ClinVar Detail
NM_003014.4(SFRP4):c.958C>A (p.Pro320Thr) AND SFRP4-related disorder ClinVar Detail
In addition, homozygosity for the minor allele of SFRP4 P320T was significantly associated with rect... DisGeNET Detail
In addition, homozygosity for the minor allele of SFRP4 P320T was significantly associated with rect... DisGeNET Detail
In addition, homozygosity for the minor allele of SFRP4 P320T was significantly associated with rect... DisGeNET 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
rs1802073 dbSNP
Genome
hg38
Position
chr7:37,907,562-37,907,562
Variant Type
snv
Reference Allele
G
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1140
Mean of sample read depth (HGVD)
40.71
Standard deviation of sample read depth (HGVD)
27.27
Number of reference allele (HGVD)
1177
Number of alternative allele (HGVD)
1103
Allele Frequency (HGVD)
0.4837719298245614
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))
rs1802073
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4964
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
8319
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
4743
East Asian Heterozygous Counts (ExAC)
2071
East Asian Homozygous Counts (ExAC)
1336
East Asian Allele Frequency (ExAC)
0.5484505087881592
Chromosome Counts in All Race (ExAC)
121344
Allele Counts in All Race (ExAC)
53174
Heterozygous Counts in All Race (ExAC)
28942
Homozygous Counts in All Race (ExAC)
12116
Allele Frequency in All Race (ExAC)
0.4382087289029536
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