chr16:3590852:G>A Detail (hg38) (SLX4)

Information

Genome

Assembly Position
hg19 chr16:3,640,853-3,640,853 View the variant detail on this assembly version.
hg38 chr16:3,590,852-3,590,852

HGVS

Type Transcript Protein
RefSeq NM_032444.2:c.2786C>T NP_115820.2:p.Pro929Leu
Ensemble ENST00000294008.4:c.2786C>T ENST00000294008.4:p.Pro929Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.021
ToMMo:0.020
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.028

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 613278 OMIM
HGNC 23845 HGNC
Ensembl ENSG00000188827 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv54461438 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-15 criteria provided, single submitter Fanconi anemia germline Detail
Benign 2018-08-03 criteria provided, single submitter not specified germline Detail
Benign 2018-01-13 criteria provided, single submitter Fanconi anemia complementation group P germline Detail
Likely benign no assertion criteria provided not provided germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_032444.4(SLX4):c.2786C>T (p.Pro929Leu) AND Fanconi anemia ClinVar Detail
NM_032444.4(SLX4):c.2786C>T (p.Pro929Leu) AND not specified ClinVar Detail
NM_032444.4(SLX4):c.2786C>T (p.Pro929Leu) AND Fanconi anemia complementation group P ClinVar Detail
NM_032444.4(SLX4):c.2786C>T (p.Pro929Leu) AND not provided 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
rs117707719 dbSNP
Genome
hg38
Position
chr16:3,590,852-3,590,852
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
137.04
Standard deviation of sample read depth (HGVD)
66.88
Number of reference allele (HGVD)
2369
Number of alternative allele (HGVD)
51
Allele Frequency (HGVD)
0.021074380165289255
Gene Symbol (HGVD)
SLX4
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))
rs117707719
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0197
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
331
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
245
East Asian Heterozygous Counts (ExAC)
241
East Asian Homozygous Counts (ExAC)
2
East Asian Allele Frequency (ExAC)
0.028310607811416685
Chromosome Counts in All Race (ExAC)
121274
Allele Counts in All Race (ExAC)
245
Heterozygous Counts in All Race (ExAC)
241
Homozygous Counts in All Race (ExAC)
2
Allele Frequency in All Race (ExAC)
0.002020218678364695
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