19-39415010-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_022835.3(PLEKHG2):āc.128T>Cā(p.Met43Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000388 in 1,597,202 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_022835.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLEKHG2 | NM_022835.3 | c.128T>C | p.Met43Thr | missense_variant | Exon 3 of 19 | ENST00000425673.6 | NP_073746.2 | |
PLEKHG2 | NM_001351694.2 | c.128T>C | p.Met43Thr | missense_variant | Exon 3 of 18 | NP_001338623.1 | ||
PLEKHG2 | NM_001351693.2 | c.110-159T>C | intron_variant | Intron 2 of 19 | NP_001338622.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000631 AC: 96AN: 152164Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000441 AC: 100AN: 226912Hom.: 0 AF XY: 0.000435 AC XY: 54AN XY: 124216
GnomAD4 exome AF: 0.000363 AC: 524AN: 1445038Hom.: 0 Cov.: 31 AF XY: 0.000380 AC XY: 272AN XY: 716562
GnomAD4 genome AF: 0.000631 AC: 96AN: 152164Hom.: 1 Cov.: 32 AF XY: 0.000767 AC XY: 57AN XY: 74340
ClinVar
Submissions by phenotype
not provided Benign:2
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PLEKHG2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at