3-319825-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006614.4(CHL1):c.49C>T(p.Leu17Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,599,498 control chromosomes in the GnomAD database, including 47,599 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006614.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHL1 | NM_006614.4 | c.49C>T | p.Leu17Phe | missense_variant | 3/28 | ENST00000256509.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHL1 | ENST00000256509.7 | c.49C>T | p.Leu17Phe | missense_variant | 3/28 | 1 | NM_006614.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.305 AC: 46229AN: 151544Hom.: 8409 Cov.: 32
GnomAD3 exomes AF: 0.254 AC: 62934AN: 247384Hom.: 9011 AF XY: 0.249 AC XY: 33323AN XY: 133776
GnomAD4 exome AF: 0.223 AC: 323554AN: 1447836Hom.: 39168 Cov.: 29 AF XY: 0.223 AC XY: 160990AN XY: 720480
GnomAD4 genome ? AF: 0.305 AC: 46305AN: 151662Hom.: 8431 Cov.: 32 AF XY: 0.305 AC XY: 22617AN XY: 74106
ClinVar
Submissions by phenotype
CHL1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 24, 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