19-19562039-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025245.3(PBX4):āc.1111A>Gā(p.Ser371Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,612,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_025245.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PBX4 | ENST00000251203.14 | c.1111A>G | p.Ser371Gly | missense_variant | 8/8 | 1 | NM_025245.3 | ENSP00000251203.5 | ||
PBX4 | ENST00000557978.6 | n.*669A>G | non_coding_transcript_exon_variant | 8/8 | 1 | ENSP00000453348.1 | ||||
PBX4 | ENST00000557978.6 | n.*669A>G | 3_prime_UTR_variant | 8/8 | 1 | ENSP00000453348.1 | ||||
PBX4 | ENST00000558276.7 | n.395A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248698Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134742
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460650Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 726618
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 25, 2024 | The c.1111A>G (p.S371G) alteration is located in exon 8 (coding exon 8) of the PBX4 gene. This alteration results from a A to G substitution at nucleotide position 1111, causing the serine (S) at amino acid position 371 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