16-24035424-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_002738.7(PRKCB):c.406A>G(p.Met136Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,622 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 Uncertain significance (★).
Frequency
Consequence
NM_002738.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKCB | NM_002738.7 | c.406A>G | p.Met136Val | missense_variant | 5/17 | ENST00000643927.1 | |
PRKCB | NM_212535.3 | c.406A>G | p.Met136Val | missense_variant | 5/17 | ||
PRKCB | XM_047434365.1 | c.19A>G | p.Met7Val | missense_variant | 4/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKCB | ENST00000643927.1 | c.406A>G | p.Met136Val | missense_variant | 5/17 | NM_002738.7 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250224Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135262
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461476Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727022
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.406A>G (p.M136V) alteration is located in exon 5 (coding exon 5) of the PRKCB gene. This alteration results from a A to G substitution at nucleotide position 406, causing the methionine (M) at amino acid position 136 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at