6-32186893-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002586.5(PBX2):c.1033G>A(p.Gly345Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000769 in 1,613,476 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002586.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PBX2 | NM_002586.5 | c.1033G>A | p.Gly345Ser | missense_variant | 7/9 | ENST00000375050.6 | NP_002577.2 | |
PBX2 | XM_047418839.1 | c.688G>A | p.Gly230Ser | missense_variant | 6/8 | XP_047274795.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PBX2 | ENST00000375050.6 | c.1033G>A | p.Gly345Ser | missense_variant | 7/9 | 1 | NM_002586.5 | ENSP00000364190.3 | ||
PBX2 | ENST00000495300.1 | n.283G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000127 AC: 32AN: 251210Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135822
GnomAD4 exome AF: 0.0000780 AC: 114AN: 1461356Hom.: 0 Cov.: 31 AF XY: 0.0000839 AC XY: 61AN XY: 726994
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.1033G>A (p.G345S) alteration is located in exon 7 (coding exon 7) of the PBX2 gene. This alteration results from a G to A substitution at nucleotide position 1033, causing the glycine (G) at amino acid position 345 to be replaced by a serine (S). 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