16-89816614-A-G
Variant summary
Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PVS1PS1_ModeratePM2PP5_Very_Strong
The NM_000135.4(FANCA):āc.2T>Cā(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000282 in 1,524,328 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (ā ā ).
Frequency
Consequence
NM_000135.4 start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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FANCA | NM_000135.4 | c.2T>C | p.Met1? | start_lost | Exon 1 of 43 | ENST00000389301.8 | NP_000126.2 | |
FANCA | NM_001286167.3 | c.2T>C | p.Met1? | start_lost | Exon 1 of 43 | NP_001273096.1 | ||
FANCA | NM_001018112.3 | c.2T>C | p.Met1? | start_lost | Exon 1 of 11 | NP_001018122.1 | ||
FANCA | NM_001351830.2 | c.2T>C | p.Met1? | start_lost | Exon 1 of 10 | NP_001338759.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152032Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000414 AC: 5AN: 120628Hom.: 0 AF XY: 0.0000745 AC XY: 5AN XY: 67104
GnomAD4 exome AF: 0.0000262 AC: 36AN: 1372296Hom.: 0 Cov.: 31 AF XY: 0.0000354 AC XY: 24AN XY: 677952
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152032Hom.: 0 Cov.: 34 AF XY: 0.0000673 AC XY: 5AN XY: 74278
ClinVar
Submissions by phenotype
Fanconi anemia complementation group A Pathogenic:8
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The start loss variant c.2T>C (p.Met1?) in FANCA gene has been reported previously in individuals affected with Fanconia anemia (Levran et al., 2005; Gille et al., 2012). In addition, other variants that also affect the initiator methionine of the FANCA mRNA (c.1A>T, c.1A>G, and c.2T>A) have been reported in individuals affected with Fanconi anemia (Chandra et al., 2005). The c.2T>C (p.Met1?) variant is reported with the allele frequency (0.004%) in the gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic. The variant is predicted to be damaging by both SIFT and PolyPhen2. The residue is conserved across species. The nucleotide change in FANCA is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -
The heterozygous p.Met1Thr variant in FANCA was identified by our study, in the compound heterozygous state with a likely pathogenic variant (ClinVar Variation ID: 582405) in one individual with Fanconi anemia. Trio exome sequencing analysis revealed that this variant was in trans with another likely pathogenic variant (ClinVar Variation ID: 582405). The p.Met1Thr variant in FANCA has been previously reported in at least six unrelated individuals with Fanconi anemia complementation group A (PMID: 28060124, PMID: 30792206, PMID: 19367192, PMID: 30031030, PMID: 23898106, PMID: 10090479, PMID: 22778927) and segregated with disease in 3 affected members in one family (PMID: 28060124), but has been identified in 0.01% (3/21056) of South Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs769479800). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. This variant has also been reported in ClinVar (Variation ID: 554309) and has been interpreted as pathogenic by Counsyl, Mayo Clinic Laboratories, GeneDx, Invitae, the Leiden Open Variant Database, Natera, Inc, and PerkinElmer Genomics. Of these six unrelated individuals who were previously reported (PMID: 28060124, PMID: 30792206, PMID: 19367192, PMID: 30031030, PMID: 23898106, PMID: 10090479, PMID: 22778927), one was a homozygote (PMID: 10090479), and four were compound heterozygotes who carried a pathogenic or likely pathogenic variants in trans (PMID: 28060124, ClinVar Variation ID: 545114; PMID: 30792206; PMID: 19367192; PMID: 23898106, ClinVar Variation ID: 41003) and one was a compound heterozygote who carried a variant of uncertain significance in trans (PMID: 30031030), and, in addition, the variant was found in trans with a pathogenic variant in the individual identified by our study (ClinVar Variation ID: 582405), which increases the likelihood that the p.Met1Thr variant is pathogenic. Five additional pathogenic or likely pathogenic variants, resulting in a different amino acid change at the same position, c.1A>G (p.Met1Val), c.1A>C (p.Met1Leu), c.1A>T (p.Met1Leu), c.2T>A (p.Met1Lys), c.2T>G (p.Met1Arg), and c.3G>T (p.Met1Ile), have been reported in association with disease in ClinVar, supporting that a change at this position may not be tolerated (Variation ID: 435134, 553521, 553965, 556239, 934462, 555802). In vitro functional studies provide some evidence that the p.Met1Thr variant may slightly impact protein function (PMID: 30031030). However, these types of assays may not accurately represent biological function. This variant is an initiation codon variant with closest in-frame potential start codon at in exon 4 at Met116 and there are 53 variants classified as pathogenic or likely pathogenic in ClinVar (access date 10/10/2022) upstream of closest in-frame potential start codon (Met116). Loss of function is an established disease mechanism of autosomal recessive Fanconi anemia complementation group A. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Fanconi anemia complementation group A. ACMG/AMP Criteria applied: PVS1_Moderate, PM3_VeryStrong, PS3_Supporting, PM5, PP1 (Richards 2015). -
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Curator: Arleen D. Auerbach. Submitters to LOVD: Arleen D. Auerbach, Johan de Winter. -
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Fanconi anemia Pathogenic:2
This sequence change affects the initiator methionine of the FANCA mRNA. The next in-frame methionine is located at codon 116. This variant is present in population databases (rs769479800, gnomAD 0.01%). Disruption of the initiator codon has been observed in individuals with Fanconi anemia (PMID: 10090479, 15643609, 16084127, 22778927, 23898106, 24584348). ClinVar contains an entry for this variant (Variation ID: 554309). For these reasons, this variant has been classified as Pathogenic. -
Variant summary: FANCA c.2T>C (p.Met1Thr) alters the initiation codon and is predicted to result either in absence of the protein or truncation of the encoded protein due to translation initiation at a downstream codon. The next in-frame methionine is located at codon 116. Three of three in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.1e-05 in 120628 control chromosomes (gnomAD). c.2T>C has been reported in the literature in multiple individuals affected with Fanconi Anemia (examples: Levran_2005, Pinto_2009, Moghrabi_2009, Gille_2012, Li_2018, and Mori_2019). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, in this study this variant was not able to fully rescue MMC sensitivity (Li_2018). The following publications have been ascertained in the context of this evaluation (PMID: 22778927, 15643609, 30031030, 19367192, 30792206, 19278965). Other start loss variants have been classified pathogenic in ClinVar (CV ID 934462, 556239, 554309). Eight submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
not provided Pathogenic:2
PVS1_Moderate, PS3, PM2, PM3 -
Identified in patients with Fanconi anemia referred for genetic testing at GeneDx and in published literature (Levran et al., 2005; Li et al., 2018; Mori et al., 2019); Published functional studies demonstrate a damaging effect (Li et al., 2018); Initiation codon variant in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 24584348, 10090479, 28060124, 30792206, 23898106, 22778927, 19367192, 16084127, 15643609, 31589614, 30031030) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at