3-142963282-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_198504.4(PAQR9):c.55G>A(p.Ala19Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,482,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_198504.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAQR9 | NM_198504.4 | c.55G>A | p.Ala19Thr | missense_variant | Exon 1 of 1 | ENST00000340634.6 | NP_940906.1 | |
PAQR9 | NM_001375300.1 | c.55G>A | p.Ala19Thr | missense_variant | Exon 2 of 4 | NP_001362229.1 | ||
PAQR9 | NM_001375301.1 | c.55G>A | p.Ala19Thr | missense_variant | Exon 2 of 4 | NP_001362230.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000791 AC: 12AN: 151774Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000232 AC: 2AN: 86246Hom.: 0 AF XY: 0.0000213 AC XY: 1AN XY: 46886
GnomAD4 exome AF: 0.00000902 AC: 12AN: 1330890Hom.: 0 Cov.: 31 AF XY: 0.00000922 AC XY: 6AN XY: 650956
GnomAD4 genome AF: 0.0000791 AC: 12AN: 151774Hom.: 0 Cov.: 33 AF XY: 0.0000540 AC XY: 4AN XY: 74114
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at