16-89811013-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_000135.4(FANCA):c.342C>T(p.Ala114=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000793 in 1,613,900 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A114A) has been classified as Likely benign.
Frequency
Consequence
NM_000135.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCA | NM_000135.4 | c.342C>T | p.Ala114= | synonymous_variant | 4/43 | ENST00000389301.8 | |
FANCA | NM_001286167.3 | c.342C>T | p.Ala114= | synonymous_variant | 4/43 | ||
FANCA | NM_001018112.3 | c.342C>T | p.Ala114= | synonymous_variant | 4/11 | ||
FANCA | NM_001351830.2 | c.342C>T | p.Ala114= | synonymous_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCA | ENST00000389301.8 | c.342C>T | p.Ala114= | synonymous_variant | 4/43 | 1 | NM_000135.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000163 AC: 41AN: 251146Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135810
GnomAD4 exome AF: 0.0000807 AC: 118AN: 1461746Hom.: 1 Cov.: 31 AF XY: 0.000100 AC XY: 73AN XY: 727158
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74328
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 22, 2017 | - - |
Fanconi anemia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Fanconi anemia complementation group A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at