rs112446681
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000490972.7(FANCC):c.1387C>T(p.Arg463Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000826 in 1,569,554 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000490972.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCC | NM_000136.3 | c.1329+175C>T | intron_variant | ENST00000289081.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCC | ENST00000289081.8 | c.1329+175C>T | intron_variant | 1 | NM_000136.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00378 AC: 575AN: 152182Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000976 AC: 177AN: 181306Hom.: 0 AF XY: 0.000727 AC XY: 73AN XY: 100456
GnomAD4 exome AF: 0.000509 AC: 721AN: 1417256Hom.: 6 Cov.: 37 AF XY: 0.000472 AC XY: 332AN XY: 703136
GnomAD4 genome ? AF: 0.00378 AC: 576AN: 152298Hom.: 3 Cov.: 33 AF XY: 0.00375 AC XY: 279AN XY: 74464
ClinVar
Submissions by phenotype
not specified Benign:1Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 07, 2014 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Fanconi anemia Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | May 10, 2017 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2023 | FANCC: BS1, BS2 - |
Fanconi anemia complementation group C Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at