16-89758581-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_000135.4(FANCA):c.2977C>A(p.Gln993Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000241 in 1,613,526 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000135.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00139 AC: 211AN: 152118Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000302 AC: 76AN: 251338Hom.: 1 AF XY: 0.000221 AC XY: 30AN XY: 135852
GnomAD4 exome AF: 0.000121 AC: 177AN: 1461290Hom.: 2 Cov.: 31 AF XY: 0.0000990 AC XY: 72AN XY: 726940
GnomAD4 genome AF: 0.00139 AC: 212AN: 152236Hom.: 1 Cov.: 32 AF XY: 0.00138 AC XY: 103AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1Other:1
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Fanconi anemia Benign:2
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Fanconi anemia complementation group A 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