chr6-35452542-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_021922.3(FANCE):c.-4C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000206 in 1,311,726 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000085 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
FANCE
NM_021922.3 5_prime_UTR
NM_021922.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.61
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 6-35452542-C-T is Benign according to our data. Variant chr6-35452542-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3047795.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCE | NM_021922.3 | c.-4C>T | 5_prime_UTR_variant | 1/10 | ENST00000229769.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCE | ENST00000229769.3 | c.-4C>T | 5_prime_UTR_variant | 1/10 | 1 | NM_021922.3 | P1 | ||
FANCE | ENST00000648059.1 | c.-4C>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/11 | |||||
FANCE | ENST00000696264.1 | upstream_gene_variant | |||||||
FANCE | ENST00000696265.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.0000856 AC: 13AN: 151930Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000121 AC: 14AN: 1159678Hom.: 0 Cov.: 30 AF XY: 0.0000107 AC XY: 6AN XY: 561604
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GnomAD4 genome AF: 0.0000855 AC: 13AN: 152048Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74330
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FANCE-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 21, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at