chr20-5923000-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001819.3(CHGB):c.856G>A(p.Gly286Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000208 in 1,610,722 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001819.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHGB | NM_001819.3 | c.856G>A | p.Gly286Arg | missense_variant | 4/5 | ENST00000378961.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHGB | ENST00000378961.9 | c.856G>A | p.Gly286Arg | missense_variant | 4/5 | 1 | NM_001819.3 | P1 | |
CHGB | ENST00000455042.1 | c.796G>A | p.Gly266Arg | missense_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000224 AC: 34AN: 152038Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000538 AC: 130AN: 241436Hom.: 0 AF XY: 0.000428 AC XY: 56AN XY: 130886
GnomAD4 exome AF: 0.000208 AC: 303AN: 1458566Hom.: 2 Cov.: 63 AF XY: 0.000186 AC XY: 135AN XY: 725332
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152156Hom.: 0 Cov.: 31 AF XY: 0.000229 AC XY: 17AN XY: 74394
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at