chr16-30902479-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001330.5(CTF1):c.546C>T(p.Arg182Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000115 in 1,479,278 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 Uncertain significance (★).
Frequency
Consequence
NM_001330.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTF1 | ENST00000279804.3 | c.546C>T | p.Arg182Arg | synonymous_variant | Exon 3 of 3 | 1 | NM_001330.5 | ENSP00000279804.2 | ||
CTF1 | ENST00000395019.3 | c.543C>T | p.Arg181Arg | synonymous_variant | Exon 3 of 3 | 1 | ENSP00000378465.3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152014Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000114 AC: 1AN: 87876Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 50102
GnomAD4 exome AF: 0.0000113 AC: 15AN: 1327264Hom.: 0 Cov.: 30 AF XY: 0.00000917 AC XY: 6AN XY: 654144
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152014Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant classified as Uncertain Significance - Favor Benign. The Arg182Arg varia nt (CFT1) has not been reported in the literature nor previously identified by o ur laboratory. This variant does not alter an amino acid, but computational tool s predict that it may create an alternate 5' splice site. Additional studies are needed to determine if the Arg182Arg variant impacts splicing and to further as sess its clinical significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at