chr1-154945716-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020524.4(PBXIP1):c.1958G>A(p.Arg653His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020524.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PBXIP1 | NM_020524.4 | c.1958G>A | p.Arg653His | missense_variant | Exon 10 of 11 | ENST00000368463.8 | NP_065385.2 | |
PBXIP1 | NM_001317734.2 | c.1871G>A | p.Arg624His | missense_variant | Exon 9 of 10 | NP_001304663.1 | ||
PBXIP1 | NM_001317735.2 | c.1493G>A | p.Arg498His | missense_variant | Exon 7 of 8 | NP_001304664.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PBXIP1 | ENST00000368463.8 | c.1958G>A | p.Arg653His | missense_variant | Exon 10 of 11 | 1 | NM_020524.4 | ENSP00000357448.3 | ||
PBXIP1 | ENST00000368465.5 | c.1871G>A | p.Arg624His | missense_variant | Exon 9 of 10 | 2 | ENSP00000357450.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250744Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135590
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461892Hom.: 0 Cov.: 34 AF XY: 0.00000825 AC XY: 6AN XY: 727246
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1958G>A (p.R653H) alteration is located in exon 10 (coding exon 9) of the PBXIP1 gene. This alteration results from a G to A substitution at nucleotide position 1958, causing the arginine (R) at amino acid position 653 to be replaced by a histidine (H). 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