chr3-319804-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_006614.4(CHL1):āc.28C>Gā(p.Leu10Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,608,120 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_006614.4 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 |
---|---|---|---|---|---|---|---|---|
CHL1 | NM_006614.4 | c.28C>G | p.Leu10Val | missense_variant | 3/28 | ENST00000256509.7 | NP_006605.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHL1 | ENST00000256509.7 | c.28C>G | p.Leu10Val | missense_variant | 3/28 | 1 | NM_006614.4 | ENSP00000256509 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000593 AC: 90AN: 151874Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000814 AC: 203AN: 249236Hom.: 1 AF XY: 0.000579 AC XY: 78AN XY: 134762
GnomAD4 exome AF: 0.000212 AC: 308AN: 1456130Hom.: 1 Cov.: 28 AF XY: 0.000168 AC XY: 122AN XY: 724568
GnomAD4 genome AF: 0.000592 AC: 90AN: 151990Hom.: 0 Cov.: 32 AF XY: 0.000606 AC XY: 45AN XY: 74288
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
CHL1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 18, 2019 | This variant is classified as likely 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