6-165876668-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000647768.3(PDE10A):c.106+109440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,118 control chromosomes in the GnomAD database, including 45,263 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 0.77 ( 45263 hom., cov: 32)
Consequence
PDE10A
ENST00000647768.3 intron
ENST00000647768.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0810
Genes affected
PDE10A (HGNC:8772): (phosphodiesterase 10A) The protein encoded by this gene belongs to the cyclic nucleotide phosphodiesterase family. It plays a role in signal transduction by regulating the intracellular concentration of cyclic nucleotides. This protein can hydrolyze both cAMP and cGMP to the corresponding nucleoside 5' monophosphate, but has higher affinity for cAMP, and is more efficient with cAMP as substrate. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Dec 2011]
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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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDE10A | XM_011535387.4 | c.58+34140C>T | intron_variant | XP_011533689.2 | ||||
PDE10A | XM_017010194.3 | c.58+34140C>T | intron_variant | XP_016865683.1 | ||||
PDE10A | XM_017010197.3 | c.58+34140C>T | intron_variant | XP_016865686.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDE10A | ENST00000366882.7 | c.-615+110861C>T | intron_variant | 5 | ENSP00000355847 | |||||
PDE10A | ENST00000647768.3 | c.106+109440C>T | intron_variant | ENSP00000497930 | A2 | |||||
PDE10A | ENST00000672859.1 | c.-308-84333C>T | intron_variant | ENSP00000500900 | A2 |
Frequencies
GnomAD3 genomes AF: 0.769 AC: 116954AN: 152000Hom.: 45221 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.769 AC: 117049AN: 152118Hom.: 45263 Cov.: 32 AF XY: 0.777 AC XY: 57755AN XY: 74348
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at