rs4713867
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_021922.3(FANCE):āc.387A>Cā(p.Pro129=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 1,613,928 control chromosomes in the GnomAD database, including 388,042 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. P129P) has been classified as Uncertain significance.
Frequency
Consequence
NM_021922.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCE | NM_021922.3 | c.387A>C | p.Pro129= | synonymous_variant | 2/10 | ENST00000229769.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCE | ENST00000229769.3 | c.387A>C | p.Pro129= | synonymous_variant | 2/10 | 1 | NM_021922.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.743 AC: 112920AN: 152008Hom.: 42567 Cov.: 32
GnomAD3 exomes AF: 0.721 AC: 181094AN: 251214Hom.: 65881 AF XY: 0.713 AC XY: 96792AN XY: 135786
GnomAD4 exome AF: 0.686 AC: 1002192AN: 1461802Hom.: 345414 Cov.: 76 AF XY: 0.686 AC XY: 498993AN XY: 727208
GnomAD4 genome AF: 0.743 AC: 113041AN: 152126Hom.: 42628 Cov.: 32 AF XY: 0.743 AC XY: 55268AN XY: 74370
ClinVar
Submissions by phenotype
Fanconi anemia complementation group E Benign:4
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 14, 2019 | - - |
Uncertain significance, no assertion criteria provided | curation | Leiden Open Variation Database | Feb 07, 2011 | Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach. - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 08, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at