6-35462869-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_021922.3(FANCE):c.1464C>T(p.Ala488=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,614,124 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 (★). Synonymous variant affecting the same amino acid position (i.e. A488A) has been classified as Likely benign.
Frequency
Consequence
NM_021922.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCE | NM_021922.3 | c.1464C>T | p.Ala488= | synonymous_variant | 9/10 | ENST00000229769.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCE | ENST00000229769.3 | c.1464C>T | p.Ala488= | synonymous_variant | 9/10 | 1 | NM_021922.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000722 AC: 11AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251494Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135922
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461874Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727236
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74386
ClinVar
Submissions by phenotype
Fanconi anemia complementation group E Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 30, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at