chr19-39173621-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005884.5(PAK4):c.709C>G(p.Leu237Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000518 in 1,543,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAK4 | NM_005884.5 | c.709C>G | p.Leu237Val | missense_variant | 5/10 | ENST00000360442.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAK4 | ENST00000360442.8 | c.709C>G | p.Leu237Val | missense_variant | 5/10 | 5 | NM_005884.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152042Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000323 AC: 6AN: 185896Hom.: 0 AF XY: 0.0000297 AC XY: 3AN XY: 100938
GnomAD4 exome AF: 0.00000503 AC: 7AN: 1391054Hom.: 0 Cov.: 33 AF XY: 0.00000584 AC XY: 4AN XY: 684804
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152042Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.709C>G (p.L237V) alteration is located in exon 6 (coding exon 3) of the PAK4 gene. This alteration results from a C to G substitution at nucleotide position 709, causing the leucine (L) at amino acid position 237 to be replaced by a valine (V). 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