rs2270962
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_018294.6(CWF19L1):c.479G>A(p.Cys160Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 1,613,390 control chromosomes in the GnomAD database, including 16,440 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_018294.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CWF19L1 | NM_018294.6 | c.479G>A | p.Cys160Tyr | missense_variant | 5/14 | ENST00000354105.10 | NP_060764.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CWF19L1 | ENST00000354105.10 | c.479G>A | p.Cys160Tyr | missense_variant | 5/14 | 1 | NM_018294.6 | ENSP00000326411.6 |
Frequencies
GnomAD3 genomes AF: 0.211 AC: 32097AN: 151974Hom.: 6307 Cov.: 32
GnomAD3 exomes AF: 0.124 AC: 31163AN: 251308Hom.: 3517 AF XY: 0.116 AC XY: 15803AN XY: 135862
GnomAD4 exome AF: 0.0889 AC: 129947AN: 1461296Hom.: 10103 Cov.: 32 AF XY: 0.0885 AC XY: 64312AN XY: 727002
GnomAD4 genome AF: 0.212 AC: 32182AN: 152094Hom.: 6337 Cov.: 32 AF XY: 0.213 AC XY: 15821AN XY: 74374
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
CWF19L1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 30, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at