chr19-39169590-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005884.5(PAK4):c.37G>T(p.Ala13Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,436 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A13V) has been classified 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAK4 | NM_005884.5 | c.37G>T | p.Ala13Ser | missense_variant | 3/10 | ENST00000360442.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAK4 | ENST00000360442.8 | c.37G>T | p.Ala13Ser | missense_variant | 3/10 | 5 | NM_005884.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000264 AC: 4AN: 151796Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 250084Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135388
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461640Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727150
GnomAD4 genome ? AF: 0.0000264 AC: 4AN: 151796Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74144
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.37G>T (p.A13S) alteration is located in exon 4 (coding exon 1) of the PAK4 gene. This alteration results from a G to T substitution at nucleotide position 37, causing the alanine (A) at amino acid position 13 to be replaced by a serine (S). 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