rs7073610
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_018294.6(CWF19L1):c.776C>T(p.Pro259Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 1,613,678 control chromosomes in the GnomAD database, including 2,439 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). 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 -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CWF19L1 | NM_018294.6 | c.776C>T | p.Pro259Leu | missense_variant | 8/14 | ENST00000354105.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CWF19L1 | ENST00000354105.10 | c.776C>T | p.Pro259Leu | missense_variant | 8/14 | 1 | NM_018294.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0632 AC: 9609AN: 152058Hom.: 350 Cov.: 33
GnomAD3 exomes AF: 0.0516 AC: 12983AN: 251384Hom.: 380 AF XY: 0.0509 AC XY: 6920AN XY: 135876
GnomAD4 exome AF: 0.0508 AC: 74267AN: 1461502Hom.: 2089 Cov.: 31 AF XY: 0.0506 AC XY: 36780AN XY: 727064
GnomAD4 genome AF: 0.0632 AC: 9616AN: 152176Hom.: 350 Cov.: 33 AF XY: 0.0634 AC XY: 4714AN XY: 74410
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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at