9-127712291-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001012502.3(CFAP157):c.1079G>A(p.Arg360Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000675 in 1,614,026 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001012502.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP157 | NM_001012502.3 | c.1079G>A | p.Arg360Gln | missense_variant | 6/9 | ENST00000373295.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP157 | ENST00000373295.7 | c.1079G>A | p.Arg360Gln | missense_variant | 6/9 | 5 | NM_001012502.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000101 AC: 25AN: 248514Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135116
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461718Hom.: 2 Cov.: 33 AF XY: 0.0000976 AC XY: 71AN XY: 727164
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.1079G>A (p.R360Q) alteration is located in exon 6 (coding exon 6) of the CFAP157 gene. This alteration results from a G to A substitution at nucleotide position 1079, causing the arginine (R) at amino acid position 360 to be replaced by a glutamine (Q). 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