rs137913973
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 4P and 5B. PM1PM2BP4_StrongBP6
The ENST00000389301.8(FANCA):āc.2267G>Cā(p.Arg756Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,593,434 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R756C) has been classified as Likely benign.
Frequency
Consequence
ENST00000389301.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FANCA | NM_000135.4 | c.2267G>C | p.Arg756Pro | missense_variant | 25/43 | ENST00000389301.8 | NP_000126.2 | |
FANCA | NM_001286167.3 | c.2267G>C | p.Arg756Pro | missense_variant | 25/43 | NP_001273096.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FANCA | ENST00000389301.8 | c.2267G>C | p.Arg756Pro | missense_variant | 25/43 | 1 | NM_000135.4 | ENSP00000373952 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000256 AC: 39AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000610 AC: 13AN: 212986Hom.: 0 AF XY: 0.0000524 AC XY: 6AN XY: 114528
GnomAD4 exome AF: 0.0000257 AC: 37AN: 1441156Hom.: 0 Cov.: 35 AF XY: 0.0000210 AC XY: 15AN XY: 714640
GnomAD4 genome AF: 0.000263 AC: 40AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74450
ClinVar
Submissions by phenotype
Fanconi anemia Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 09, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 23, 2020 | - - |
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Nov 18, 2022 | PM2 - |
Likely benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Oct 28, 2022 | - - |
Fanconi anemia complementation group A Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Dec 22, 2020 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at