6-165336194-G-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS1
The NM_001385079.1(PDE10A):c.2994C>T(p.Ala998=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000377 in 1,613,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00039 ( 0 hom. )
Consequence
PDE10A
NM_001385079.1 synonymous
NM_001385079.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.93
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 -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.31).
BP6
Variant 6-165336194-G-A is Benign according to our data. Variant chr6-165336194-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 747132.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.93 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000223 (34/152178) while in subpopulation EAS AF= 0.00136 (7/5148). AF 95% confidence interval is 0.000638. There are 0 homozygotes in gnomad4. There are 11 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDE10A | NM_001385079.1 | c.2994C>T | p.Ala998= | synonymous_variant | 21/22 | ENST00000539869.4 | NP_001372008.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDE10A | ENST00000539869.4 | c.2994C>T | p.Ala998= | synonymous_variant | 21/22 | 1 | NM_001385079.1 | ENSP00000438284 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000224 AC: 34AN: 152060Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000247 AC: 62AN: 251236Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135834
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GnomAD4 exome AF: 0.000393 AC: 575AN: 1461552Hom.: 0 Cov.: 30 AF XY: 0.000370 AC XY: 269AN XY: 727092
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GnomAD4 genome AF: 0.000223 AC: 34AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74388
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 09, 2022 | - - |
Computational scores
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Benign
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at