rs4951338
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014935.5(PLEKHA6):c.524+382T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,102 control chromosomes in the GnomAD database, including 28,713 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 0.61 ( 28713 hom., cov: 32)
Consequence
PLEKHA6
NM_014935.5 intron
NM_014935.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0640
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHA6 | NM_014935.5 | c.524+382T>C | intron_variant | ENST00000272203.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHA6 | ENST00000272203.8 | c.524+382T>C | intron_variant | 1 | NM_014935.5 | P2 | |||
PLEKHA6 | ENST00000414478.1 | c.584+382T>C | intron_variant | 5 | |||||
PLEKHA6 | ENST00000637508.1 | c.524+382T>C | intron_variant | 5 | A2 | ||||
PLEKHA6 | ENST00000672625.1 | c.650+382T>C | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.610 AC: 92726AN: 151984Hom.: 28675 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.610 AC: 92809AN: 152102Hom.: 28713 Cov.: 32 AF XY: 0.619 AC XY: 45989AN XY: 74348
GnomAD4 genome
?
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92809
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152102
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32
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45989
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74348
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Asia WGS
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2367
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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