chr19-39173366-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005884.5(PAK4):c.653G>A(p.Arg218Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000562 in 1,529,462 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 Uncertain significance (★).
Frequency
Consequence
NM_005884.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAK4 | NM_005884.5 | c.653G>A | p.Arg218Gln | missense_variant | 4/10 | ENST00000360442.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAK4 | ENST00000360442.8 | c.653G>A | p.Arg218Gln | missense_variant | 4/10 | 5 | NM_005884.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 152000Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000166 AC: 28AN: 169140Hom.: 0 AF XY: 0.000108 AC XY: 10AN XY: 92566
GnomAD4 exome AF: 0.0000545 AC: 75AN: 1377344Hom.: 0 Cov.: 33 AF XY: 0.0000607 AC XY: 41AN XY: 675648
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.653G>A (p.R218Q) alteration is located in exon 5 (coding exon 2) of the PAK4 gene. This alteration results from a G to A substitution at nucleotide position 653, causing the arginine (R) at amino acid position 218 to be replaced by a glutamine (Q). 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