1-204223531-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_014935.5(PLEKHA6):c.3086C>T(p.Ala1029Val) variant causes a missense change. The variant allele was found at a frequency of 0.0084 in 1,550,594 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0059 ( 9 hom., cov: 31)
Exomes 𝑓: 0.0087 ( 89 hom. )
Consequence
PLEKHA6
NM_014935.5 missense
NM_014935.5 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 4.33
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0027147233).
BP6
Variant 1-204223531-G-A is Benign according to our data. Variant chr1-204223531-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2639826.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLEKHA6 | NM_014935.5 | c.3086C>T | p.Ala1029Val | missense_variant | 22/23 | ENST00000272203.8 | NP_055750.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLEKHA6 | ENST00000272203.8 | c.3086C>T | p.Ala1029Val | missense_variant | 22/23 | 1 | NM_014935.5 | ENSP00000272203 | P2 | |
PLEKHA6 | ENST00000637508.1 | c.3458C>T | p.Ala1153Val | missense_variant | 26/27 | 5 | ENSP00000490182 | A2 | ||
PLEKHA6 | ENST00000414478.1 | c.3146C>T | p.Ala1049Val | missense_variant | 22/23 | 5 | ENSP00000402046 |
Frequencies
GnomAD3 genomes AF: 0.00592 AC: 899AN: 151802Hom.: 8 Cov.: 31
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GnomAD3 exomes AF: 0.00690 AC: 1084AN: 157134Hom.: 20 AF XY: 0.00715 AC XY: 591AN XY: 82680
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GnomAD4 exome AF: 0.00867 AC: 12123AN: 1398674Hom.: 89 Cov.: 31 AF XY: 0.00847 AC XY: 5843AN XY: 689916
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GnomAD4 genome AF: 0.00592 AC: 899AN: 151920Hom.: 9 Cov.: 31 AF XY: 0.00536 AC XY: 398AN XY: 74210
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | PLEKHA6: BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.
MutationTaster
Benign
N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N
REVEL
Benign
Sift
Benign
T;.;T
Sift4G
Benign
T;.;T
Polyphen
B;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at