rs775822054
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000135.4(FANCA):c.324C>T(p.Pro108=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,876 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P108P) has been classified as Likely benign.
Frequency
Consequence
NM_000135.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCA | NM_000135.4 | c.324C>T | p.Pro108= | synonymous_variant | 4/43 | ENST00000389301.8 | |
FANCA | NM_001286167.3 | c.324C>T | p.Pro108= | synonymous_variant | 4/43 | ||
FANCA | NM_001018112.3 | c.324C>T | p.Pro108= | synonymous_variant | 4/11 | ||
FANCA | NM_001351830.2 | c.324C>T | p.Pro108= | synonymous_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCA | ENST00000389301.8 | c.324C>T | p.Pro108= | synonymous_variant | 4/43 | 1 | NM_000135.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251038Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135782
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461730Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727146
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74318
ClinVar
Submissions by phenotype
Fanconi anemia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at