chr19-19570744-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_025245.3(PBX4):c.283A>G(p.Arg95Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000293 in 1,613,986 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PBX4 | NM_025245.3 | c.283A>G | p.Arg95Gly | missense_variant | 3/8 | ENST00000251203.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PBX4 | ENST00000251203.14 | c.283A>G | p.Arg95Gly | missense_variant | 3/8 | 1 | NM_025245.3 | P1 | |
PBX4 | ENST00000557978.6 | c.283A>G | p.Arg95Gly | missense_variant, NMD_transcript_variant | 3/8 | 1 | |||
PBX4 | ENST00000559735.1 | n.251A>G | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
PBX4 | ENST00000558222.1 | c.283A>G | p.Arg95Gly | missense_variant, NMD_transcript_variant | 3/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152130Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251446Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135912
GnomAD4 exome AF: 0.000314 AC: 459AN: 1461856Hom.: 1 Cov.: 31 AF XY: 0.000279 AC XY: 203AN XY: 727232
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152130Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.283A>G (p.R95G) alteration is located in exon 3 (coding exon 3) of the PBX4 gene. This alteration results from a A to G substitution at nucleotide position 283, causing the arginine (R) at amino acid position 95 to be replaced by a glycine (G). 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