chr19-39414144-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_022835.3(PLEKHG2):c.58G>T(p.Gly20Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000683 in 1,551,564 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022835.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLEKHG2 | NM_022835.3 | c.58G>T | p.Gly20Cys | missense_variant | Exon 2 of 19 | ENST00000425673.6 | NP_073746.2 | |
PLEKHG2 | NM_001351693.2 | c.58G>T | p.Gly20Cys | missense_variant | Exon 2 of 20 | NP_001338622.1 | ||
PLEKHG2 | NM_001351694.2 | c.58G>T | p.Gly20Cys | missense_variant | Exon 2 of 18 | NP_001338623.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152266Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 26AN: 155974Hom.: 1 AF XY: 0.000230 AC XY: 19AN XY: 82694
GnomAD4 exome AF: 0.0000715 AC: 100AN: 1399180Hom.: 3 Cov.: 30 AF XY: 0.000106 AC XY: 73AN XY: 690122
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152384Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74530
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.58G>T (p.G20C) alteration is located in exon 2 (coding exon 1) of the PLEKHG2 gene. This alteration results from a G to T substitution at nucleotide position 58, causing the glycine (G) at amino acid position 20 to be replaced by a cysteine (C). 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