1-204229007-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014935.5(PLEKHA6):c.2681G>A(p.Arg894Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014935.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLEKHA6 | NM_014935.5 | c.2681G>A | p.Arg894Gln | missense_variant | 19/23 | ENST00000272203.8 | NP_055750.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLEKHA6 | ENST00000272203.8 | c.2681G>A | p.Arg894Gln | missense_variant | 19/23 | 1 | NM_014935.5 | ENSP00000272203 | P2 | |
PLEKHA6 | ENST00000637508.1 | c.3053G>A | p.Arg1018Gln | missense_variant | 23/27 | 5 | ENSP00000490182 | A2 | ||
PLEKHA6 | ENST00000414478.1 | c.2741G>A | p.Arg914Gln | missense_variant | 19/23 | 5 | ENSP00000402046 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251460Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135904
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461876Hom.: 0 Cov.: 33 AF XY: 0.0000316 AC XY: 23AN XY: 727242
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2024 | The c.2681G>A (p.R894Q) alteration is located in exon 19 (coding exon 17) of the PLEKHA6 gene. This alteration results from a G to A substitution at nucleotide position 2681, causing the arginine (R) at amino acid position 894 to be replaced by a glutamine (Q). 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