rs142377616
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_000135.4(FANCA):c.3031C>T(p.Arg1011Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000731 in 1,614,036 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 Likely benign (★★).
Frequency
Consequence
NM_000135.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000115 AC: 29AN: 251456Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135914
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461842Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727226
GnomAD4 genome AF: 0.000125 AC: 19AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74410
ClinVar
Submissions by phenotype
Fanconi anemia complementation group A Pathogenic:1Benign:1
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Curator: Arleen D. Auerbach. Submitter to LOVD: Myungshin Kim. -
Fanconi anemia Benign:1
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Ovarian cancer Benign:1
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FANCA-related disorder Benign:1
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). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at