rs17334002
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014935.5(PLEKHA6):c.-95+22713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,232 control chromosomes in the GnomAD database, including 3,382 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 0.19 ( 3382 hom., cov: 32)
Consequence
PLEKHA6
NM_014935.5 intron
NM_014935.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.19
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=-0.75).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHA6 | NM_014935.5 | c.-95+22713A>G | intron_variant | ENST00000272203.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHA6 | ENST00000272203.8 | c.-95+22713A>G | intron_variant | 1 | NM_014935.5 | P2 | |||
PLEKHA6 | ENST00000414478.1 | c.-95+22713A>G | intron_variant | 5 | |||||
PLEKHA6 | ENST00000564627.2 | c.218+30818A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.193 AC: 29409AN: 152114Hom.: 3381 Cov.: 32
GnomAD3 genomes
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29409
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152114
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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: 0.193 AC: 29415AN: 152232Hom.: 3382 Cov.: 32 AF XY: 0.195 AC XY: 14511AN XY: 74426
GnomAD4 genome
?
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29415
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152232
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32
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14511
AN XY:
74426
Gnomad4 AFR
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Asia WGS
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639
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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