chr1-204228185-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014935.5(PLEKHA6):c.2929G>A(p.Val977Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,612,308 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLEKHA6 | NM_014935.5 | c.2929G>A | p.Val977Met | missense_variant | 21/23 | ENST00000272203.8 | NP_055750.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLEKHA6 | ENST00000272203.8 | c.2929G>A | p.Val977Met | missense_variant | 21/23 | 1 | NM_014935.5 | ENSP00000272203 | P2 | |
PLEKHA6 | ENST00000637508.1 | c.3301G>A | p.Val1101Met | missense_variant | 25/27 | 5 | ENSP00000490182 | A2 | ||
PLEKHA6 | ENST00000414478.1 | c.2989G>A | p.Val997Met | missense_variant | 21/23 | 5 | ENSP00000402046 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 250124Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135188
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1460004Hom.: 0 Cov.: 31 AF XY: 0.0000152 AC XY: 11AN XY: 726048
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | The c.2929G>A (p.V977M) alteration is located in exon 21 (coding exon 19) of the PLEKHA6 gene. This alteration results from a G to A substitution at nucleotide position 2929, causing the valine (V) at amino acid position 977 to be replaced by a methionine (M). 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