19-19570822-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_025245.3(PBX4):c.205C>T(p.Arg69Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,613,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025245.3 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 |
---|---|---|---|---|---|---|---|
PBX4 | NM_025245.3 | c.205C>T | p.Arg69Cys | missense_variant | 3/8 | ENST00000251203.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PBX4 | ENST00000251203.14 | c.205C>T | p.Arg69Cys | missense_variant | 3/8 | 1 | NM_025245.3 | P1 | |
PBX4 | ENST00000557978.6 | c.205C>T | p.Arg69Cys | missense_variant, NMD_transcript_variant | 3/8 | 1 | |||
PBX4 | ENST00000559735.1 | n.173C>T | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
PBX4 | ENST00000558222.1 | c.205C>T | p.Arg69Cys | missense_variant, NMD_transcript_variant | 3/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251216Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135788
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461738Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 727164
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.205C>T (p.R69C) alteration is located in exon 3 (coding exon 3) of the PBX4 gene. This alteration results from a C to T substitution at nucleotide position 205, causing the arginine (R) at amino acid position 69 to be replaced by a cysteine (C). 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