4-2449736-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001193282.4(CFAP99):c.709C>T(p.Arg237Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000165 in 1,536,178 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R237H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001193282.4 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 |
---|---|---|---|---|---|---|---|
CFAP99 | NM_001193282.4 | c.709C>T | p.Arg237Cys | missense_variant | 7/16 | ENST00000635017.2 | |
CFAP99 | XM_047415685.1 | c.709C>T | p.Arg237Cys | missense_variant | 7/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP99 | ENST00000635017.2 | c.709C>T | p.Arg237Cys | missense_variant | 7/16 | 5 | NM_001193282.4 | P1 | |
CFAP99 | ENST00000511731.5 | n.486C>T | non_coding_transcript_exon_variant | 5/6 | 1 | ||||
CFAP99 | ENST00000514556.5 | n.291C>T | non_coding_transcript_exon_variant | 3/4 | 5 | ||||
CFAP99 | ENST00000515732.1 | n.276C>T | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000499 AC: 76AN: 152186Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000119 AC: 16AN: 134916Hom.: 0 AF XY: 0.0000817 AC XY: 6AN XY: 73396
GnomAD4 exome AF: 0.000129 AC: 178AN: 1383874Hom.: 0 Cov.: 31 AF XY: 0.000105 AC XY: 72AN XY: 682882
GnomAD4 genome AF: 0.000499 AC: 76AN: 152304Hom.: 0 Cov.: 31 AF XY: 0.000457 AC XY: 34AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.709C>T (p.R237C) alteration is located in exon 7 (coding exon 6) of the CFAP99 gene. This alteration results from a C to T substitution at nucleotide position 709, causing the arginine (R) at amino acid position 237 to be replaced by a cysteine (C). 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