16-89816614-A-G

Position:

• chr16-89816614-A-G

Variant summary

Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PVS1 PS1_Moderate PM2 PP5_Very_Strong

The ENST00000389301.8(FANCA):​c.2T>C​(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 Pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.000046 (0 hom., cov: 34)
  • Exomes 𝑓: 0.000026 (0 hom.)
• Consequence: FANCA ENST00000389301.8 start_lost
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:10
• Conservation: PhyloP100: 1.06

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]

ACMG classification

Verdict is Pathogenic. Variant got 20 ACMG points.

• PVS1: Start lost variant, no new inframe start found.
• PS1: Another start lost variant in ENST00000389301.8 (FANCA) was described as [Conflicting_classifications_of_pathogenicity] in ClinVar as 555802
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 16-89816614-A-G is Pathogenic according to our data. Variant chr16-89816614-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 554309.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-89816614-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FANCA	NM_000135.4	c.2T>C	p.Met1?	start_lost	1/43	ENST00000389301.8	NP_000126.2
FANCA	NM_001286167.3	c.2T>C	p.Met1?	start_lost	1/43		NP_001273096.1
FANCA	NM_001018112.3	c.2T>C	p.Met1?	start_lost	1/11		NP_001018122.1
FANCA	NM_001351830.2	c.2T>C	p.Met1?	start_lost	1/10		NP_001338759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FANCA	ENST00000389301.8	c.2T>C	p.Met1?	start_lost	1/43	1	NM_000135.4	ENSP00000373952	P1

Frequencies

GnomAD3 genomes AF: 0.0000460 AC: 7 AN: 152032 Hom.: 0 Cov.: 34

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.0000944

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000414 AC: 5 AN: 120628 Hom.: 0 AF XY: 0.0000745 AC XY: 5 AN XY: 67104

Gnomad AFR exome AF: 0.000313

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000142

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000211

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000262 AC: 36 AN: 1372296 Hom.: 0 Cov.: 31 AF XY: 0.0000354 AC XY: 24 AN XY: 677952

Gnomad4 AFR exome AF: 0.0000343

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000167

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000186

Gnomad4 OTH exome AF: 0.0000349

GnomAD4 genome AF: 0.0000460 AC: 7 AN: 152032 Hom.: 0 Cov.: 34 AF XY: 0.0000673 AC XY: 5 AN XY: 74278

Gnomad4 AFR AF: 0.0000483

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.0000944

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000435 Hom.: 0

Bravo AF: 0.0000113

ExAC AF: 0.0000320 AC: 3

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Fanconi anemia complementation group A Pathogenic:6

Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Oct 25, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Mar 26, 2021	- -
Pathogenic, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 25, 2023	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). -
Pathogenic, no assertion criteria provided	curation	Leiden Open Variation Database	Feb 28, 2020	Curator: Arleen D. Auerbach. Submitters to LOVD: Arleen D. Auerbach, Johan de Winter. -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	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. -

Fanconi anemia Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 30, 2024	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 27, 2023	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

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Nov 28, 2022	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) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Apr 14, 2020	PVS1_Moderate, PS3, PM2, PM3 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Pathogenic	0.27
CADD	Benign	17
DANN	Benign	0.83
DEOGEN2	Benign	0.090	T;.;.;T;T;.
Eigen	Benign	-0.0089
Eigen_PC	Benign	-0.12
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.90	D;D;D;D;D;D
M_CAP	Pathogenic	0.99	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D
MetaSVM	Uncertain	0.31	D
MutationTaster	Benign	1.0	D;D;D;D
PROVEAN	Benign	-1.2	N;N;N;N;N;N
REVEL	Uncertain	0.45
Sift	Pathogenic	0.0	D;D;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D
Polyphen		0.90	P;.;.;.;D;D
Vest4		0.74
MutPred		1.0		Gain of phosphorylation at M1 (P = 0.0319);Gain of phosphorylation at M1 (P = 0.0319);Gain of phosphorylation at M1 (P = 0.0319);Gain of phosphorylation at M1 (P = 0.0319);Gain of phosphorylation at M1 (P = 0.0319);Gain of phosphorylation at M1 (P = 0.0319);
MVP		0.91
ClinPred		0.98	D
GERP RS		4.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6
Varity_R		0.92
gMVP		0.24

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs769479800; hg19: chr16-89883022;