16-89740839-AG-A
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000135.4(FANCA):c.3792delC(p.Leu1265fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,404 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. S1264S) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
FANCA
NM_000135.4 frameshift
NM_000135.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00800
Publications
1 publications found
Genes affected
FANCA (HGNC:3582): (FA complementation group A) The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (also called BRIP1), FANCL, FANCM and FANCN (also called PALB2). The previously defined group FANCH is the same as FANCA. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The members of the Fanconi anemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. This gene encodes the protein for complementation group A. Alternative splicing results in multiple transcript variants encoding different isoforms. Mutations in this gene are the most common cause of Fanconi anemia. [provided by RefSeq, Jul 2008]
ZNF276 (HGNC:23330): (zinc finger protein 276) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in kinetochore. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 16-89740839-AG-A is Pathogenic according to our data. Variant chr16-89740839-AG-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 134273.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-89740839-AG-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 134273.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-89740839-AG-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 134273.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-89740839-AG-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 134273.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-89740839-AG-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 134273.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-89740839-AG-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 134273.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-89740839-AG-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 134273.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-89740839-AG-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 134273.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-89740839-AG-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 134273.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-89740839-AG-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 134273.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FANCA | ENST00000389301.8 | c.3792delC | p.Leu1265fs | frameshift_variant | Exon 38 of 43 | 1 | NM_000135.4 | ENSP00000373952.3 | ||
| ZNF276 | ENST00000443381.7 | c.*2595delG | 3_prime_UTR_variant | Exon 11 of 11 | 1 | NM_001113525.2 | ENSP00000415836.2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461404Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726950 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461404
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
726950
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33458
American (AMR)
AF:
AC:
1
AN:
44702
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26130
East Asian (EAS)
AF:
AC:
0
AN:
39688
South Asian (SAS)
AF:
AC:
0
AN:
86186
European-Finnish (FIN)
AF:
AC:
0
AN:
53368
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111728
Other (OTH)
AF:
AC:
0
AN:
60376
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:2Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Fanconi anemia Pathogenic:1
Jul 27, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 134273). This variant has not been reported in the literature in individuals affected with FANCA-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu1265*) in the FANCA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FANCA are known to be pathogenic (PMID: 19367192). -
Fanconi anemia complementation group A Pathogenic:1
Mar 14, 2023
Baylor Genetics
Significance:Likely pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
not specified Other:1
Sep 19, 2013
ITMI
Significance:not provided
Review Status:no classification provided
Collection Method:reference population
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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