2-219010021-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_194302.4(CFAP65):c.4373G>A(p.Arg1458His) variant causes a missense change. The variant allele was found at a frequency of 0.00022 in 1,612,470 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_194302.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CFAP65 | ENST00000341552.10 | c.4373G>A | p.Arg1458His | missense_variant | Exon 27 of 35 | 5 | NM_194302.4 | ENSP00000340776.5 | ||
CFAP65 | ENST00000453220.5 | c.4373G>A | p.Arg1458His | missense_variant | Exon 25 of 33 | 5 | ENSP00000409117.1 | |||
ENSG00000224090 | ENST00000441450.1 | n.151C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152072Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000381 AC: 95AN: 249602Hom.: 1 AF XY: 0.000407 AC XY: 55AN XY: 135260
GnomAD4 exome AF: 0.000214 AC: 313AN: 1460280Hom.: 3 Cov.: 31 AF XY: 0.000220 AC XY: 160AN XY: 726394
GnomAD4 genome AF: 0.000276 AC: 42AN: 152190Hom.: 1 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74418
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4373G>A (p.R1458H) alteration is located in exon 27 (coding exon 25) of the CFAP65 gene. This alteration results from a G to A substitution at nucleotide position 4373, causing the arginine (R) at amino acid position 1458 to be replaced by a histidine (H). 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