chr10-122429681-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001001974.4(PLEKHA1):āc.958A>Gā(p.Thr320Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 1,613,732 control chromosomes in the GnomAD database, including 323,997 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001001974.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHA1 | NM_001001974.4 | c.958A>G | p.Thr320Ala | missense_variant | 12/12 | ENST00000368990.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHA1 | ENST00000368990.8 | c.958A>G | p.Thr320Ala | missense_variant | 12/12 | 1 | NM_001001974.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.685 AC: 104048AN: 151792Hom.: 36275 Cov.: 30
GnomAD3 exomes AF: 0.681 AC: 171087AN: 251314Hom.: 59095 AF XY: 0.674 AC XY: 91542AN XY: 135824
GnomAD4 exome AF: 0.624 AC: 911762AN: 1461822Hom.: 287680 Cov.: 73 AF XY: 0.626 AC XY: 454995AN XY: 727198
GnomAD4 genome AF: 0.686 AC: 104151AN: 151910Hom.: 36317 Cov.: 30 AF XY: 0.693 AC XY: 51412AN XY: 74224
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at