chr16:23607907:C>T Detail (hg38) (PALB2)

Information

Genome

Assembly Position
hg19 chr16:23,619,228-23,619,228 View the variant detail on this assembly version.
hg38 chr16:23,607,907-23,607,907

HGVS

Type Transcript Protein
RefSeq NM_024675.3:c.3307G>A NP_078951.2:p.Val1103Met
Ensemble ENST00000261584.9:c.3307G>A ENST00000261584.9:p.Val1103Met
ENST00000561514.3:c.3313G>A ENST00000561514.3:p.Val1105Met
Summary

MGeND

Clinical significance Likely benign Uncertain significance
Variant entry 4
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 610355 OMIM
HGNC 26144 HGNC
Ensembl ENSG00000083093 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv55054130 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Likely benign 2023/03/20 cervix uteri, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Likely benign 2023/03/20 other germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Likely benign 2023/03/20 colon, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Uncertain significance other germline MGS000069
(TMGS000141) 		Kenjiro Kosaki
 Keio University
Okayama University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2024-02-01 criteria provided, conflicting interpretations Familial cancer of breast germline unknown Detail
Conflicting interpretations of pathogenicity 2021-11-01 criteria provided, conflicting interpretations Hereditary cancer-predisposing syndrome germline Detail
Conflicting interpretations of pathogenicity 2023-09-11 criteria provided, conflicting interpretations not specified germline Detail
Conflicting interpretations of pathogenicity 2022-06-13 criteria provided, conflicting interpretations not provided germline unknown Detail
Uncertain significance 2019-05-01 criteria provided, single submitter hereditary breast ovarian cancer syndrome germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_024675.4(PALB2):c.3307G>A (p.Val1103Met) AND Familial cancer of breast ClinVar Detail
NM_024675.4(PALB2):c.3307G>A (p.Val1103Met) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_024675.4(PALB2):c.3307G>A (p.Val1103Met) AND not specified ClinVar Detail
NM_024675.4(PALB2):c.3307G>A (p.Val1103Met) AND not provided ClinVar Detail
NM_024675.4(PALB2):c.3307G>A (p.Val1103Met) AND Hereditary breast ovarian cancer syndrome 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
rs201657283 dbSNP
Genome
hg38
Position
chr16:23,607,907-23,607,907
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
859
Mean of sample read depth (HGVD)
17.07
Standard deviation of sample read depth (HGVD)
18.85
Number of reference allele (HGVD)
1715
Number of alternative allele (HGVD)
3
Allele Frequency (HGVD)
0.0017462165308498253
Gene Symbol (HGVD)
PALB2
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))
rs201657283
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0006
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10
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)
3
East Asian Heterozygous Counts (ExAC)
3
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
3.4666050381326557E-4
Chromosome Counts in All Race (ExAC)
121402
Allele Counts in All Race (ExAC)
8
Heterozygous Counts in All Race (ExAC)
8
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
6.589677270555675E-5
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