chr16-88643375-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4BP6_Moderate
The NM_000101.4(CYBA):c.566C>G(p.Pro189Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000098 in 1,530,720 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. P189L) has been classified as Uncertain significance.
Frequency
Consequence
NM_000101.4 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 |
---|---|---|---|---|---|---|---|
CYBA | NM_000101.4 | c.566C>G | p.Pro189Arg | missense_variant | 6/6 | ENST00000261623.8 | |
CYBA | XM_011522905.4 | c.*1791C>G | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYBA | ENST00000261623.8 | c.566C>G | p.Pro189Arg | missense_variant | 6/6 | 1 | NM_000101.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152084Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000233 AC: 28AN: 120168Hom.: 0 AF XY: 0.000241 AC XY: 16AN XY: 66502
GnomAD4 exome AF: 0.0000834 AC: 115AN: 1378636Hom.: 0 Cov.: 32 AF XY: 0.0000883 AC XY: 60AN XY: 679774
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152084Hom.: 0 Cov.: 33 AF XY: 0.000363 AC XY: 27AN XY: 74296
ClinVar
Submissions by phenotype
Granulomatous disease, chronic, autosomal recessive, cytochrome b-negative Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 25, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at