NM_000135.4:c.80-13C>T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_000135.4(FANCA):c.80-13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000804 in 1,602,378 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000135.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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FANCA | NM_000135.4 | c.80-13C>T | intron_variant | Intron 1 of 42 | ENST00000389301.8 | NP_000126.2 | ||
FANCA | NM_001286167.3 | c.80-13C>T | intron_variant | Intron 1 of 42 | NP_001273096.1 | |||
FANCA | NM_001018112.3 | c.80-13C>T | intron_variant | Intron 1 of 10 | NP_001018122.1 | |||
FANCA | NM_001351830.2 | c.80-13C>T | intron_variant | Intron 1 of 9 | NP_001338759.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00118 AC: 180AN: 152248Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.000964 AC: 242AN: 251132Hom.: 2 AF XY: 0.00116 AC XY: 158AN XY: 135842
GnomAD4 exome AF: 0.000766 AC: 1110AN: 1450012Hom.: 4 Cov.: 27 AF XY: 0.000828 AC XY: 598AN XY: 722176
GnomAD4 genome AF: 0.00117 AC: 178AN: 152366Hom.: 2 Cov.: 31 AF XY: 0.00133 AC XY: 99AN XY: 74510
ClinVar
Submissions by phenotype
Fanconi anemia complementation group A Uncertain:1Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
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Fanconi anemia Benign:2
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not specified Benign:1Other:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at