rs369052148
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_000136.3(FANCC):c.166-7T>C variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.0000485 in 1,609,444 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_000136.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCC | NM_000136.3 | c.166-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000289081.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCC | ENST00000289081.8 | c.166-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000136.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000243 AC: 37AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000840 AC: 21AN: 249902Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135134
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1457238Hom.: 0 Cov.: 29 AF XY: 0.0000262 AC XY: 19AN XY: 725292
GnomAD4 genome ? AF: 0.000243 AC: 37AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74350
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Fanconi anemia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Fanconi anemia complementation group A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at