6-165638020-G-T

Position:

• chr6-165638020-G-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+23927C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,810 control chromosomes in the GnomAD database, including 3,723 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 0.22 (3723 hom., cov: 32)
• Consequence: PDE10A NM_001385079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407

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]

PDE10A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE10A	NM_001385079.1	c.865+23927C>A		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+23927C>A		intron_variant		1	NM_001385079.1	ENSP00000438284.3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32870 AN: 151694 Hom.: 3722 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.00618

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.217 AC: 32877 AN: 151810 Hom.: 3723 Cov.: 32 AF XY: 0.216 AC XY: 16011 AN XY: 74186

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.00619

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.243

Alfa AF: 0.228 Hom.: 8361

Bravo AF: 0.215

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.63
DANN	Benign	0.67

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: rs2983516; hg19: chr6-166051508; COSMIC: COSV64840526;