rs769779495
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_021922.3(FANCE):c.246G>A(p.Glu82=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,315,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_021922.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCE | NM_021922.3 | c.246G>A | p.Glu82= | splice_region_variant, synonymous_variant | 1/10 | ENST00000229769.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCE | ENST00000229769.3 | c.246G>A | p.Glu82= | splice_region_variant, synonymous_variant | 1/10 | 1 | NM_021922.3 | P1 | |
FANCE | ENST00000696264.1 | c.246G>A | p.Glu82= | splice_region_variant, synonymous_variant | 1/8 | ||||
FANCE | ENST00000648059.1 | c.246G>A | p.Glu82= | splice_region_variant, synonymous_variant, NMD_transcript_variant | 1/11 | ||||
FANCE | ENST00000696265.1 | c.246G>A | p.Glu82= | splice_region_variant, synonymous_variant, NMD_transcript_variant | 1/9 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 1AN: 35924Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 21676
GnomAD4 exome AF: 0.0000327 AC: 38AN: 1162994Hom.: 0 Cov.: 30 AF XY: 0.0000301 AC XY: 17AN XY: 563934
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74374
ClinVar
Submissions by phenotype
Fanconi anemia complementation group E Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 25, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
FANCE-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 30, 2021 | 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at