chr5:86675592:C>A Detail (hg19) (CCNH, RASA1)

Information

Genome

Assembly Position
hg19 chr5:86,675,592-86,675,592
hg38 chr5:87,379,775-87,379,775 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_022650.2:c.1997C>A NP_072179.1:p.Thr666Asn
NM_002890.2:c.2528C>A NP_002881.1:p.Thr843Asn
Ensemble ENST00000456692.6:c.1997C>A ENST00000456692.6:p.Thr666Asn
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.007
ToMMo:0.007
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.013

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 139150 OMIM
HGNC 9871 HGNC
Ensembl ENSG00000145715 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv21809717 TogoVar
COSMIC COSM3975654 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely benign 2016-06-14 criteria provided, single submitter Capillary malformation-arteriovenous malformation 1 germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Parkes Weber syndrome germline Detail
Benign 2024-01-28 criteria provided, single submitter Capillary malformation-arteriovenous malformation syndrome germline Detail
Benign Likely benign 2023-03-27 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2018-12-04 criteria provided, single submitter germline Detail
Benign 2020-03-11 criteria provided, single submitter RASA1-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_002890.3(RASA1):c.2528C>A (p.Thr843Asn) AND Capillary malformation-arteriovenous malformation 1 ClinVar Detail
NM_002890.3(RASA1):c.2528C>A (p.Thr843Asn) AND Parkes Weber syndrome ClinVar Detail
NM_002890.3(RASA1):c.2528C>A (p.Thr843Asn) AND Capillary malformation-arteriovenous malformation syn... ClinVar Detail
NM_002890.3(RASA1):c.2528C>A (p.Thr843Asn) AND not provided ClinVar Detail
NM_002890.3(RASA1):c.2528C>A (p.Thr843Asn) AND Cardiovascular phenotype ClinVar Detail
NM_002890.3(RASA1):c.2528C>A (p.Thr843Asn) AND RASA1-related disorder 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
rs184201084 dbSNP
Genome
hg19
Position
chr5:86,675,592-86,675,592
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1206
Mean of sample read depth (HGVD)
54.38
Standard deviation of sample read depth (HGVD)
27.73
Number of reference allele (HGVD)
2395
Number of alternative allele (HGVD)
17
Allele Frequency (HGVD)
0.007048092868988391
Gene Symbol (HGVD)
RASA1
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))
rs184201084
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0069
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
115
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8534
East Asian Allele Counts (ExAC)
114
East Asian Heterozygous Counts (ExAC)
108
East Asian Homozygous Counts (ExAC)
3
East Asian Allele Frequency (ExAC)
0.013358331380360909
Chromosome Counts in All Race (ExAC)
120548
Allele Counts in All Race (ExAC)
160
Heterozygous Counts in All Race (ExAC)
152
Homozygous Counts in All Race (ExAC)
4
Allele Frequency in All Race (ExAC)
0.0013272721239672165
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