rs1358786

Positions:

• chr6-165641434-A-G
• chr6-165641434-A-T

Variant summary

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

The NM_001385079.1(PDE10A):​c.865+20513T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,140 control chromosomes in the GnomAD database, including 53,211 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 0.83 (53211 hom., cov: 31)
• Consequence: PDE10A NM_001385079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE10A	NM_001385079.1	c.865+20513T>C		intron_variant		ENST00000539869.4	NP_001372008.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE10A	ENST00000539869.4	c.865+20513T>C		intron_variant		1	NM_001385079.1	ENSP00000438284	P3

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126859 AN: 152022 Hom.: 53165 Cov.: 31

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.835 AC: 126963 AN: 152140 Hom.: 53211 Cov.: 31 AF XY: 0.837 AC XY: 62219 AN XY: 74374

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.839

Alfa AF: 0.855 Hom.: 23767

Bravo AF: 0.835

Asia WGS AF: 0.812 AC: 2821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.55

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: rs1358786; hg19: chr6-166054922; COSMIC: COSV64831806;