rs17333933
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014935.5(PLEKHA6):c.-95+39042A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 160,772 control chromosomes in the GnomAD database, including 7,838 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.31 ( 7337 hom., cov: 32)
Exomes 𝑓: 0.33 ( 501 hom. )
Consequence
PLEKHA6
NM_014935.5 intron
NM_014935.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.43
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHA6 | NM_014935.5 | c.-95+39042A>C | intron_variant | ENST00000272203.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHA6 | ENST00000272203.8 | c.-95+39042A>C | intron_variant | 1 | NM_014935.5 | P2 | |||
PLEKHA6 | ENST00000414478.1 | c.-95+39042A>C | intron_variant | 5 | |||||
PLEKHA6 | ENST00000564627.2 | c.219-45843A>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.306 AC: 46430AN: 151966Hom.: 7317 Cov.: 32
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GnomAD4 exome AF: 0.326 AC: 2837AN: 8690Hom.: 501 AF XY: 0.321 AC XY: 1379AN XY: 4300
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GnomAD4 genome ? AF: 0.306 AC: 46481AN: 152082Hom.: 7337 Cov.: 32 AF XY: 0.306 AC XY: 22731AN XY: 74326
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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