chr11-64925902-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006244.4(PPP2R5B):āc.168G>Cā(p.Gln56His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,611,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. Q56Q) has been classified as Likely benign.
Frequency
Consequence
NM_006244.4 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 |
---|---|---|---|---|---|---|---|
PPP2R5B | NM_006244.4 | c.168G>C | p.Gln56His | missense_variant | 2/14 | ENST00000164133.7 | |
PPP2R5B | XM_047427199.1 | c.168G>C | p.Gln56His | missense_variant | 1/13 | ||
PPP2R5B | XM_011545132.3 | c.81G>C | p.Gln27His | missense_variant | 3/15 | ||
PPP2R5B | XM_047427200.1 | c.81G>C | p.Gln27His | missense_variant | 3/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R5B | ENST00000164133.7 | c.168G>C | p.Gln56His | missense_variant | 2/14 | 1 | NM_006244.4 | P1 | |
PPP2R5B | ENST00000526559.5 | c.168G>C | p.Gln56His | missense_variant | 2/5 | 5 | |||
PPP2R5B | ENST00000532850.1 | c.-91G>C | 5_prime_UTR_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248092Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134982
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1459718Hom.: 0 Cov.: 34 AF XY: 0.00000826 AC XY: 6AN XY: 726158
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2022 | The c.168G>C (p.Q56H) alteration is located in exon 2 (coding exon 1) of the PPP2R5B gene. This alteration results from a G to C substitution at nucleotide position 168, causing the glutamine (Q) at amino acid position 56 to be replaced by a histidine (H). 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