NM_021922.3:c.229C>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021922.3(FANCE):c.229C>A(p.Pro77Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000567 in 1,301,090 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 Uncertain significance (★★).
Frequency
Consequence
NM_021922.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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FANCE | ENST00000229769.3 | c.229C>A | p.Pro77Thr | missense_variant | Exon 1 of 10 | 1 | NM_021922.3 | ENSP00000229769.2 | ||
FANCE | ENST00000696264.1 | c.229C>A | p.Pro77Thr | missense_variant | Exon 1 of 8 | ENSP00000512511.1 | ||||
FANCE | ENST00000648059.1 | n.229C>A | non_coding_transcript_exon_variant | Exon 1 of 11 | ENSP00000497902.1 | |||||
FANCE | ENST00000696265.1 | n.229C>A | non_coding_transcript_exon_variant | Exon 1 of 9 | ENSP00000512512.1 |
Frequencies
GnomAD3 genomes AF: 0.000663 AC: 101AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000403 AC: 11AN: 27270Hom.: 0 AF XY: 0.000421 AC XY: 7AN XY: 16616
GnomAD4 exome AF: 0.000555 AC: 637AN: 1148742Hom.: 0 Cov.: 30 AF XY: 0.000553 AC XY: 307AN XY: 555160
GnomAD4 genome AF: 0.000663 AC: 101AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.000564 AC XY: 42AN XY: 74500
ClinVar
Submissions by phenotype
not provided Uncertain:3
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In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 26580448, 25188385, 24728327, 27153395, 29146900) -
Fanconi anemia complementation group E Uncertain:3
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 77 of the FANCE protein (p.Pro77Thr). This variant is present in population databases (rs587778335, gnomAD 0.09%). This variant has not been reported in the literature in individuals affected with FANCE-related conditions. ClinVar contains an entry for this variant (Variation ID: 134330). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt FANCE protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
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not specified Uncertain:1Other:1
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FANCE-related disorder Uncertain:1
The FANCE c.229C>A variant is predicted to result in the amino acid substitution p.Pro77Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.10% of alleles in individuals of European (Non-Finnish) descent in gnomAD Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Fanconi anemia Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at