chr11-77340638-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002576.5(PAK1):c.1116+8C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 1,442,560 control chromosomes in the GnomAD database, including 78,620 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002576.5 splice_region, intron
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 |
---|---|---|---|---|---|---|---|
PAK1 | NM_002576.5 | c.1116+8C>G | splice_region_variant, intron_variant | ENST00000356341.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAK1 | ENST00000356341.8 | c.1116+8C>G | splice_region_variant, intron_variant | 1 | NM_002576.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.247 AC: 37480AN: 152000Hom.: 5669 Cov.: 32
GnomAD3 exomes AF: 0.294 AC: 73835AN: 250914Hom.: 12293 AF XY: 0.311 AC XY: 42152AN XY: 135610
GnomAD4 exome AF: 0.327 AC: 422375AN: 1290440Hom.: 72951 Cov.: 20 AF XY: 0.332 AC XY: 216574AN XY: 651432
GnomAD4 genome ? AF: 0.246 AC: 37484AN: 152120Hom.: 5669 Cov.: 32 AF XY: 0.245 AC XY: 18238AN XY: 74374
ClinVar
Submissions by phenotype
PAK1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 30, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Intellectual developmental disorder with macrocephaly, seizures, and speech delay Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 16, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at