4-2462603-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001193282.4(CFAP99):āc.1822C>Gā(p.Arg608Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000206 in 1,405,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001193282.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
CFAP99 | NM_001193282.4 | c.1822C>G | p.Arg608Gly | missense_variant, splice_region_variant | 15/16 | ENST00000635017.2 | |
CFAP99 | XM_047415685.1 | c.1822C>G | p.Arg608Gly | missense_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP99 | ENST00000635017.2 | c.1822C>G | p.Arg608Gly | missense_variant, splice_region_variant | 15/16 | 5 | NM_001193282.4 | P1 | |
RNF4 | ENST00000503659.5 | c.-160C>G | splice_region_variant, 5_prime_UTR_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151924Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000191 AC: 24AN: 1253846Hom.: 0 Cov.: 33 AF XY: 0.0000260 AC XY: 16AN XY: 614756
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152032Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2023 | The c.1822C>G (p.R608G) alteration is located in exon 15 (coding exon 14) of the CFAP99 gene. This alteration results from a C to G substitution at nucleotide position 1822, causing the arginine (R) at amino acid position 608 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at