6-35452547-TGGCGACACCG-T

Position:

• chr6-35452547-TGGCGACACCG-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1 PS1_Moderate PM2 PP5_Moderate

The NM_021922.3(FANCE):​c.4_13del​(p.Ala2_?5) variant causes a frameshift, start lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: FANCE NM_021922.3 frameshift, start_lost
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 1.92

Genes affected

FANCE (HGNC:3586): (FA complementation group E) 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 E. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 38 pathogenic variants in the truncated region.
• PS1: Another start lost variant in NM_021922.3 (FANCE) was described as [Conflicting_classifications_of_pathogenicity] in ClinVar as 1060674
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 6-35452547-TGGCGACACCG-T is Pathogenic according to our data. Variant chr6-35452547-TGGCGACACCG-T is described in ClinVar as [Pathogenic]. Clinvar id is 2798486.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FANCE	NM_021922.3	c.4_13del	p.Ala2_?5	frameshift_variant, start_lost	1/10	ENST00000229769.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FANCE	ENST00000229769.3	c.4_13del	p.Ala2_?5	frameshift_variant, start_lost	1/10	1	NM_021922.3	P1
FANCE	ENST00000696264.1	c.4_13del	p.Ala2_?5	frameshift_variant, start_lost	1/8
FANCE	ENST00000648059.1	c.4_13del	p.Ala2_?5	frameshift_variant, start_lost, NMD_transcript_variant	1/11
FANCE	ENST00000696265.1	c.4_13del	p.Ala2_?5	frameshift_variant, start_lost, NMD_transcript_variant	1/9

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Fanconi anemia complementation group E Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 15, 2023

This sequence change creates a premature translational stop signal (p.Ala2Thrfs*79) in the FANCE gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FANCE are known to be pathogenic (PMID: 11001585, 17924555). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with FANCE-related conditions. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-35420324;