16-24123911-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS2
The NM_002738.7(PRKCB):c.995G>C(p.Gly332Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00026 in 1,614,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002738.7 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 |
---|---|---|---|---|---|---|---|
PRKCB | NM_002738.7 | c.995G>C | p.Gly332Ala | missense_variant | 9/17 | ENST00000643927.1 | |
PRKCB | NM_212535.3 | c.995G>C | p.Gly332Ala | missense_variant | 9/17 | ||
PRKCB | XM_047434365.1 | c.608G>C | p.Gly203Ala | missense_variant | 8/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCB | ENST00000643927.1 | c.995G>C | p.Gly332Ala | missense_variant | 9/17 | NM_002738.7 | A1 | ||
PRKCB | ENST00000321728.12 | c.995G>C | p.Gly332Ala | missense_variant | 9/17 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000191 AC: 48AN: 251424Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135880
GnomAD4 exome AF: 0.000265 AC: 388AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.000271 AC XY: 197AN XY: 727236
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74336
ClinVar
Submissions by phenotype
PRKCB-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 25, 2023 | The PRKCB c.995G>C variant is predicted to result in the amino acid substitution p.Gly332Ala. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.036% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/16-24135232-G-C). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | PRKCB: PP2, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at