chr9-96655110-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153698.2(PRXL2C):c.172G>A(p.Ala58Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000659 in 151,756 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRXL2C | NM_153698.2 | c.172G>A | p.Ala58Thr | missense_variant | Exon 1 of 6 | ENST00000375234.8 | NP_714542.1 | |
PRXL2C | XM_005251783.4 | c.172G>A | p.Ala58Thr | missense_variant | Exon 1 of 5 | XP_005251840.1 | ||
PRXL2C | XM_005251784.5 | c.30+142G>A | intron_variant | Intron 1 of 5 | XP_005251841.1 | |||
PRXL2C | XM_047422905.1 | c.30+142G>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.172G>A | p.Ala58Thr | missense_variant | Exon 1 of 6 | 1 | NM_153698.2 | ENSP00000364382.3 | ||
PRXL2C | ENST00000446045.1 | c.51+142G>A | intron_variant | Intron 1 of 5 | 1 | ENSP00000398933.1 | ||||
PRXL2C | ENST00000464512.1 | n.-138G>A | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151756Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1280046Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 630404
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151756Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74122
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.172G>A (p.A58T) 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 172, causing the alanine (A) at amino acid position 58 to be replaced by a threonine (T). 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