rs34810717
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_016734.3(PAX5):c.964G>A(p.Ala322Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0127 in 1,611,354 control chromosomes in the GnomAD database, including 160 homozygotes. 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 Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_016734.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX5 | NM_016734.3 | c.964G>A | p.Ala322Thr | missense_variant | 8/10 | ENST00000358127.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX5 | ENST00000358127.9 | c.964G>A | p.Ala322Thr | missense_variant | 8/10 | 1 | NM_016734.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00841 AC: 1279AN: 152068Hom.: 9 Cov.: 31
GnomAD3 exomes AF: 0.00970 AC: 2356AN: 242998Hom.: 21 AF XY: 0.00977 AC XY: 1288AN XY: 131828
GnomAD4 exome AF: 0.0132 AC: 19192AN: 1459168Hom.: 151 Cov.: 31 AF XY: 0.0129 AC XY: 9373AN XY: 725630
GnomAD4 genome ? AF: 0.00840 AC: 1279AN: 152186Hom.: 9 Cov.: 31 AF XY: 0.00782 AC XY: 582AN XY: 74402
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 10, 2021 | This variant is associated with the following publications: (PMID: 24728327) - |
not specified Benign:1Other:1
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at