rs758380315
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000229769.3(FANCE):c.1278G>A(p.Met426Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,614,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M426V) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000229769.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FANCE | NM_021922.3 | c.1278G>A | p.Met426Ile | missense_variant | 7/10 | ENST00000229769.3 | NP_068741.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FANCE | ENST00000229769.3 | c.1278G>A | p.Met426Ile | missense_variant | 7/10 | 1 | NM_021922.3 | ENSP00000229769 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251482Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135916
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 46AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
Fanconi anemia complementation group E Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at