rs650490

chr6-165491803-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001385079.1(PDE10A):c.995-9460T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,368 control chromosomes in the GnomAD database, including 6,629 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 0.29 (6629 hom., cov: 31)
• Consequence: PDE10A NM_001385079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE10A	NM_001385079.1	c.995-9460T>G		intron_variant		ENST00000539869.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE10A	ENST00000539869.4	c.995-9460T>G		intron_variant		1	NM_001385079.1	P3

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43640 AN: 151250 Hom.: 6610 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.279

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.289 AC: 43706 AN: 151368 Hom.: 6629 Cov.: 31 AF XY: 0.287 AC XY: 21257 AN XY: 73950

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.280

Alfa AF: 0.289 Hom.: 719

Bravo AF: 0.297

Asia WGS AF: 0.297 AC: 1033 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	3.5
Dann	Benign	0.90

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs650490; hg19: chr6-165905291;