16-89739526-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_000135.4(FANCA):c.3962G>A(p.Arg1321His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000258 in 1,551,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 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. R1321C) has been classified as Likely benign.
Frequency
Consequence
NM_000135.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCA | NM_000135.4 | c.3962G>A | p.Arg1321His | missense_variant | 40/43 | ENST00000389301.8 | |
ZNF276 | NM_001113525.2 | c.*1280C>T | 3_prime_UTR_variant | 11/11 | ENST00000443381.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCA | ENST00000389301.8 | c.3962G>A | p.Arg1321His | missense_variant | 40/43 | 1 | NM_000135.4 | P1 | |
ZNF276 | ENST00000443381.7 | c.*1280C>T | 3_prime_UTR_variant | 11/11 | 1 | NM_001113525.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000193 AC: 3AN: 155550Hom.: 0 AF XY: 0.0000122 AC XY: 1AN XY: 82102
GnomAD4 exome AF: 0.0000186 AC: 26AN: 1398998Hom.: 0 Cov.: 33 AF XY: 0.0000130 AC XY: 9AN XY: 690046
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74360
ClinVar
Submissions by phenotype
Fanconi anemia Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | Jul 05, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 17, 2023 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Feb 03, 2020 | - - |
Fanconi anemia complementation group A Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 02, 2021 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Feb 07, 2023 | In the published literature, the variant has been reported in individuals with pancreatic cancer (PMID: 28767289 (2017)) and diffuse large B cell lymphoma (PMID: 23960188 (2013)).The frequency of this variant in the general population, 0.00023 (4/17352 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at