3-58884595-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001394063.1(CFAP20DC):c.665G>A(p.Arg222His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,613,784 control chromosomes in the GnomAD database, including 131 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001394063.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CFAP20DC | NM_001394063.1 | c.665G>A | p.Arg222His | missense_variant | 7/17 | ENST00000482387.7 | NP_001380992.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CFAP20DC | ENST00000482387.7 | c.665G>A | p.Arg222His | missense_variant | 7/17 | 5 | NM_001394063.1 | ENSP00000417122.2 |
Frequencies
GnomAD3 genomes AF: 0.00727 AC: 1105AN: 152036Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00739 AC: 1859AN: 251390Hom.: 12 AF XY: 0.00809 AC XY: 1099AN XY: 135862
GnomAD4 exome AF: 0.0113 AC: 16508AN: 1461630Hom.: 121 Cov.: 31 AF XY: 0.0114 AC XY: 8260AN XY: 727126
GnomAD4 genome AF: 0.00726 AC: 1104AN: 152154Hom.: 10 Cov.: 32 AF XY: 0.00706 AC XY: 525AN XY: 74388
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at