chr3-328292-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4BP6_Moderate
The NM_006614.4(CHL1):c.323G>A(p.Arg108His) variant causes a missense change. The variant allele was found at a frequency of 0.0000434 in 1,612,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R108L) has been classified as Likely benign.
Frequency
Consequence
NM_006614.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHL1 | NM_006614.4 | c.323G>A | p.Arg108His | missense_variant | 5/28 | ENST00000256509.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHL1 | ENST00000256509.7 | c.323G>A | p.Arg108His | missense_variant | 5/28 | 1 | NM_006614.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152046Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000679 AC: 17AN: 250338Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135304
GnomAD4 exome AF: 0.0000432 AC: 63AN: 1459986Hom.: 0 Cov.: 30 AF XY: 0.0000496 AC XY: 36AN XY: 726298
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152046Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74270
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 07, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at