chr2-177675473-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_016953.4(PDE11A):c.2469G>A(p.Pro823=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,078 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 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
PDE11A
NM_016953.4 synonymous
NM_016953.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.02
Genes affected
PDE11A (HGNC:8773): (phosphodiesterase 11A) The 3',5'-cyclic nucleotides cAMP and cGMP function as second messengers in a wide variety of signal transduction pathways. 3',5'-cyclic nucleotide phosphodiesterases (PDEs) catalyze the hydrolysis of cAMP and cGMP to the corresponding 5'-monophosphates and provide a mechanism to downregulate cAMP and cGMP signaling. This gene encodes a member of the PDE protein superfamily. Mutations in this gene are a cause of Cushing disease and adrenocortical hyperplasia. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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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=-0.21).
BP6
?
Variant 2-177675473-C-T is Benign according to our data. Variant chr2-177675473-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 749915.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.02 with no splicing effect.
BS2
?
High AC in GnomAdExome at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE11A | NM_016953.4 | c.2469G>A | p.Pro823= | synonymous_variant | 17/20 | ENST00000286063.11 | |
PDE11A-AS1 | NR_136171.1 | n.104+2048C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE11A | ENST00000286063.11 | c.2469G>A | p.Pro823= | synonymous_variant | 17/20 | 1 | NM_016953.4 | P1 | |
PDE11A-AS1 | ENST00000653062.1 | n.365+21690C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152092Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251072Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135674
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GnomAD4 exome AF: 0.0000233 AC: 34AN: 1460986Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 726868
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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 | Invitae | Jun 14, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
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