chr9-96655152-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_153698.2(PRXL2C):c.130G>A(p.Gly44Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,312,634 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153698.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRXL2C | NM_153698.2 | c.130G>A | p.Gly44Arg | missense_variant | Exon 1 of 6 | ENST00000375234.8 | NP_714542.1 | |
PRXL2C | XM_005251783.4 | c.130G>A | p.Gly44Arg | missense_variant | Exon 1 of 5 | XP_005251840.1 | ||
PRXL2C | XM_005251784.5 | c.30+100G>A | intron_variant | Intron 1 of 5 | XP_005251841.1 | |||
PRXL2C | XM_047422905.1 | c.30+100G>A | intron_variant | Intron 1 of 4 | XP_047278861.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRXL2C | ENST00000375234.8 | c.130G>A | p.Gly44Arg | missense_variant | Exon 1 of 6 | 1 | NM_153698.2 | ENSP00000364382.3 | ||
PRXL2C | ENST00000446045.1 | c.51+100G>A | intron_variant | Intron 1 of 5 | 1 | ENSP00000398933.1 | ||||
PRXL2C | ENST00000464512.1 | n.-180G>A | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000146 AC: 22AN: 150880Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000309 AC: 2AN: 6482Hom.: 0 AF XY: 0.000248 AC XY: 1AN XY: 4038
GnomAD4 exome AF: 0.000211 AC: 245AN: 1161754Hom.: 1 Cov.: 31 AF XY: 0.000218 AC XY: 123AN XY: 563978
GnomAD4 genome AF: 0.000146 AC: 22AN: 150880Hom.: 0 Cov.: 32 AF XY: 0.000109 AC XY: 8AN XY: 73678
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.130G>A (p.G44R) alteration is located in exon 1 (coding exon 1) of the AAED1 gene. This alteration results from a G to A substitution at nucleotide position 130, causing the glycine (G) at amino acid position 44 to be replaced by an arginine (R). 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