chrX-27461233-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_207319.4(PPP4R3C):c.2064T>C(p.Asp688=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000779 in 513,250 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000090 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.0000075 ( 0 hom. 1 hem. )
Consequence
PPP4R3C
NM_207319.4 synonymous
NM_207319.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.374
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant X-27461233-A-G is Benign according to our data. Variant chrX-27461233-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2660212.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.374 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP4R3C | NM_207319.4 | c.2064T>C | p.Asp688= | synonymous_variant | 1/1 | ENST00000412172.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP4R3C | ENST00000412172.4 | c.2064T>C | p.Asp688= | synonymous_variant | 1/1 | NM_207319.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000896 AC: 1AN: 111612Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33782
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GnomAD4 exome AF: 0.00000747 AC: 3AN: 401638Hom.: 0 Cov.: 0 AF XY: 0.00000671 AC XY: 1AN XY: 149046
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | PPP4R3C: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at