chr20-5922495-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001819.3(CHGB):c.351G>C(p.Lys117Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,613,310 control chromosomes in the GnomAD database, including 1,802 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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_001819.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHGB | NM_001819.3 | c.351G>C | p.Lys117Asn | missense_variant | 4/5 | ENST00000378961.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHGB | ENST00000378961.9 | c.351G>C | p.Lys117Asn | missense_variant | 4/5 | 1 | NM_001819.3 | P1 | |
CHGB | ENST00000455042.1 | c.291G>C | p.Lys97Asn | missense_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0618 AC: 9399AN: 152078Hom.: 968 Cov.: 32
GnomAD3 exomes AF: 0.0166 AC: 4147AN: 249540Hom.: 382 AF XY: 0.0127 AC XY: 1718AN XY: 134950
GnomAD4 exome AF: 0.00704 AC: 10281AN: 1461114Hom.: 831 Cov.: 37 AF XY: 0.00627 AC XY: 4557AN XY: 726732
GnomAD4 genome ? AF: 0.0618 AC: 9412AN: 152196Hom.: 971 Cov.: 32 AF XY: 0.0588 AC XY: 4378AN XY: 74414
ClinVar
Submissions by phenotype
CHGB-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 28, 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