chr3-10098930-C-A
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The ENST00000287647.7(FANCD2):c.4396C>A(p.Pro1466Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000315 in 1,614,148 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1466L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000287647.7 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00165 AC: 251AN: 152148Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000418 AC: 105AN: 251460 AF XY: 0.000324 show subpopulations
GnomAD4 exome AF: 0.000176 AC: 258AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.000149 AC XY: 108AN XY: 727240 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00165 AC: 251AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.00156 AC XY: 116AN XY: 74442 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Fanconi anemia Benign:2
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not specified Benign:1Other:1
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Fanconi anemia complementation group D2 Benign:1
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not provided Benign:1
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FANCD2-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at