rs577636020

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000389301.8(FANCA):​c.2602-9_2602-8del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000571 in 1,613,836 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00043 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00058 ( 0 hom. )

Consequence

FANCA
ENST00000389301.8 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3U:8B:1

Conservation

PhyloP100: 0.996
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FANCANM_000135.4 linkuse as main transcriptc.2602-9_2602-8del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000389301.8 NP_000126.2
FANCANM_001286167.3 linkuse as main transcriptc.2602-9_2602-8del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant NP_001273096.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FANCAENST00000389301.8 linkuse as main transcriptc.2602-9_2602-8del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_000135.4 ENSP00000373952 P1O15360-1

Frequencies

GnomAD3 genomes
AF:
0.000434
AC:
66
AN:
152240
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000965
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000941
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000661
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000713
AC:
179
AN:
251154
Hom.:
0
AF XY:
0.000707
AC XY:
96
AN XY:
135782
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.0000578
Gnomad ASJ exome
AF:
0.000397
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000980
Gnomad FIN exome
AF:
0.00171
Gnomad NFE exome
AF:
0.000864
Gnomad OTH exome
AF:
0.00114
GnomAD4 exome
AF:
0.000585
AC:
855
AN:
1461596
Hom.:
0
AF XY:
0.000589
AC XY:
428
AN XY:
727090
show subpopulations
Gnomad4 AFR exome
AF:
0.000209
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.000612
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00103
Gnomad4 FIN exome
AF:
0.00210
Gnomad4 NFE exome
AF:
0.000532
Gnomad4 OTH exome
AF:
0.000596
GnomAD4 genome
AF:
0.000434
AC:
66
AN:
152240
Hom.:
0
Cov.:
33
AF XY:
0.000336
AC XY:
25
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.0000965
Gnomad4 AMR
AF:
0.000262
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000941
Gnomad4 NFE
AF:
0.000661
Gnomad4 OTH
AF:
0.000478
Alfa
AF:
0.000654
Hom.:
0
Bravo
AF:
0.000400
EpiCase
AF:
0.00104
EpiControl
AF:
0.000474

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:3Uncertain:8Benign:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Fanconi anemia Pathogenic:1Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitterclinical testingSt. Jude Molecular Pathology, St. Jude Children's Research HospitalDec 09, 2021- -
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 29, 2024- -
Likely pathogenic, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineFeb 02, 2023The c.2602-9_2602-8delCT variant in FANCA has been reported in two individuals with Fanconi anemia both of whom were compound heterozygous for the variant and a large deletion of FANCA on the other allele (Kimble 2018 PMID: 29098742). It has also been reported in 2 individuals with early-onset renal cell carcinoma, 1 child with neuroblastoma and a distant family history of cancer, and 2 breast cancer patients (initial diagnosis < 55 yrs for both) (Truong 2021 PMID: 34654685, Fiala 2021 PMID: 34308366, del Valle 2020 PMID: 32235514). It was also identified in 0.07% (45/68038) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org), and is reported in ClinVar (Variation ID 237041). RT-PCR analysis lymphoblastoid cell lines derived from one of the Fanconi anemia patients suggests that the variant results in aberrant splicing, and thus would be expected to lead to a truncated or absent protein. Loss of function of the FANCA gene is an established disease mechanism for autosomal recessive Fanconi anemia. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal recessive Fanconi anemia. ACMG/AMP criteria applied: PM3, PS3, PP4. -
not provided Uncertain:3
Uncertain significance, criteria provided, single submitterclinical testingQuest Diagnostics Nichols Institute San Juan CapistranoJul 20, 2023In the published literature, the variant has been reported in individuals with breast cancer (PMID: 32235514 (2020), 30306255 (2018), 30426508 (2018)), renal cell carcinoma (PMID: 34654685 (2021)), and Fanconi Anemia (PMID: 29098742 (2018)). This variant has been shown to result in aberrant splicing with skipping of exons 28-30 and exon 29 of the FANCA gene (PMID: 29098742 (2018)). The frequency of this variant in the general population, 0.00088 (113/128910 chromosomes in European (Non-Finnish) subpopulation, http://gnomad.broadinstitute.org), is higher than would generally be expected for pathogenic variants in this gene. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on FANCA mRNA splicing yielded inconclusive findings . Based on the available information, we are unable to determine the clinical significance of this variant. -
Uncertain significance, criteria provided, single submitterclinical testingGeneDxJun 25, 2024Reported in two individuals from related families with Fanconi anemia who also have a multi-exon deletion on the opposite allele (in trans); RNA testing in one family suggests this variant leads to aberrant splicing (PMID: 29098742); In silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 25589003, 34426522, 30426508, 34308366, 32235514, 34654685, 30306255, 29098742) -
Uncertain significance, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2024FANCA: PM3, PM2:Supporting, PS3:Supporting, BP4 -
Fanconi anemia complementation group A Pathogenic:2
Likely pathogenic, criteria provided, single submitterresearchDepartment of Pediatrics, Memorial Sloan Kettering Cancer CenterDec 15, 2020- -
Likely pathogenic, criteria provided, single submittercurationLaboratory of Medical Genetics, National & Kapodistrian University of AthensFeb 01, 2024- -
not specified Uncertain:2
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpMar 01, 2023Variant summary: FANCA c.2602-9_2602-8delCT alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, the variant has been shown to cause aberrant splicing in a patient derived cell line carrying the variant (Kimble_2018). The variant allele was found at a frequency of 0.00071 in 251154 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in FANCA causing Fanconi Anemia (0.00071 vs 0.0022), allowing no conclusion about variant significance. c.2602-9_2602-8delCT has been reported in the literature in individuals affected with Fanconi Anemia (Kimble_2018) and also in breast cancer patients (Bonache_2018, DelValle_2020, Schubert_2019). These reports do not provide unequivocal conclusions about the variant significance. This variant and FANCA c.1074_1075del/p.Tyr359fs (CV ID: 237032, classified pathogenic) has been observed in an unaffected adult internally. Eight ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (n=5), likely pathogenic (n=2) or benign (n=1). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Uncertain significance, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoDec 16, 2019DNA sequence analysis of the FANCA gene demonstrated a sequence change in intron 27, c.2602-9_2602-8del. This sequence change has been described in the gnomAD database with a frequency of 0.17% in European populations (dbSNP rs577636020). This sequence change, in addition to a large pathogenic deletion, has been identified in a Fanconi anemia family. RNA analysis of these individuals demonstrated skipping of exons 28-30 in the presence of this sequence change (PMID: 29098742). This sequence change is also predicted to have a deleterious effect on splicing based on in silico splice prediction programs. The functional significance of this sequence change is not known at present. -
FANCA-related disorder Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesMay 21, 2024The FANCA c.2602-9_2602-8delCT variant is predicted to result in an intronic deletion. This variant has been reported in two related individuals with Fanconi anemia (FA) who also harbored a partial deletion of FANCA on the opposite allele (Kimble et al. 2018. PubMed ID: 29098742). This variant has also been reported in several individuals with cancer (Bonache et al. 2018. PubMed ID: 30306255; Schubert et al. 2019. PubMed ID: 30426508; Del Valle et al. 2020. PubMed ID: 32235514; Fiala et al. 2021. PubMed ID: 34308366), although some of these individuals also have pathogenic variants in other genes associated with increased cancer risk (see Truong et al. 2021. PubMed ID: 34654685). In silico splicing prediction programs indicate that this variant weakens the adjacent canonical acceptor site (Alamut Visual Plus v1.6.1; SpliceAI, Jaganathan et al. 2019. PubMed ID: 30661751), and RNA analysis confirmed the presence of altered splice variants in FA patient cell lines (Kimble et al. 2018. PubMed ID: 29098742). A different study in patients with suspected hereditary cancer disorders stated that normal splicing was observed but did not provide supporting data for review (Del Valle et al. 2020. PubMed ID: 32235514). This variant is reported in 0.17% (42 of 25,108) of alleles in individuals of European (Finnish) descent in gnomAD but only occurs in 0.063% (162 of 257,444) of alleles in non-Finnish populations. Taken together, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.25
Details are displayed if max score is > 0.2
DS_AL_spliceai
0.25
Position offset: -7

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs577636020; hg19: chr16-89831481; API