chr6-165336155-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001385079.1(PDE10A):c.3033C>G(p.Leu1011=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,613,932 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0072 ( 13 hom., cov: 32)
Exomes 𝑓: 0.00079 ( 13 hom. )
Consequence
PDE10A
NM_001385079.1 synonymous
NM_001385079.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00800
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 6-165336155-G-C is Benign according to our data. Variant chr6-165336155-G-C is described in ClinVar as [Benign]. Clinvar id is 786541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-165336155-G-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=0.008 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00722 (1100/152300) while in subpopulation AFR AF= 0.0252 (1048/41556). AF 95% confidence interval is 0.024. There are 13 homozygotes in gnomad4. There are 533 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 13 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE10A | NM_001385079.1 | c.3033C>G | p.Leu1011= | synonymous_variant | 21/22 | ENST00000539869.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE10A | ENST00000539869.4 | c.3033C>G | p.Leu1011= | synonymous_variant | 21/22 | 1 | NM_001385079.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00722 AC: 1099AN: 152182Hom.: 13 Cov.: 32
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GnomAD3 exomes AF: 0.00174 AC: 437AN: 251360Hom.: 6 AF XY: 0.00126 AC XY: 171AN XY: 135876
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GnomAD4 exome AF: 0.000790 AC: 1154AN: 1461632Hom.: 13 Cov.: 30 AF XY: 0.000633 AC XY: 460AN XY: 727120
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
PDE10A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 02, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at