chr16:89574826:A>G Detail (hg19) (SPG7, LOC130059818)

Information

Genome

Assembly Position
hg19 chr16:89,574,826-89,574,826
hg38 chr16:89,508,418-89,508,418 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_199367.2:c.1A>G NP_955399.1:p.?
NM_003119.3:c.1A>G NP_003110.1:p.?
Ensemble ENST00000644781.1:c.1A>G ENST00000644781.1:p.?
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Pathogenic Likely pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 602783 OMIM
HGNC 11237 HGNC
Ensembl ENSG00000197912 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv56629547 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic Likely pathogenic 2023-10-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Pathogenic 2023-09-19 criteria provided, single submitter hereditary spastic paraplegia 7 germline Detail
Pathogenic 2023-07-10 criteria provided, single submitter SPG7-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.560 SPASTIC PARAPLEGIA 7, AUTOSOMAL RECESSIVE NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003119.4(SPG7):c.1A>G (p.Met1Val) AND not provided ClinVar Detail
NM_003119.4(SPG7):c.1A>G (p.Met1Val) AND Hereditary spastic paraplegia 7 ClinVar Detail
NM_003119.4(SPG7):c.1A>G (p.Met1Val) AND SPG7-related disorder ClinVar Detail
NA 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
rs794726906 dbSNP
Genome
hg19
Position
chr16:89,574,826-89,574,826
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs794726906
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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