rs7762160

Positions:

• chr6-165601943-T-C

Variant summary

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

The NM_001385079.1(PDE10A):​c.866-58375A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,038 control chromosomes in the GnomAD database, including 10,383 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 0.36 (10383 hom., cov: 32)
• Consequence: PDE10A NM_001385079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

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 (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE10A	NM_001385079.1	c.866-58375A>G		intron_variant		ENST00000539869.4	NP_001372008.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE10A	ENST00000539869.4	c.866-58375A>G		intron_variant		1	NM_001385079.1	ENSP00000438284	P3

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55336 AN: 151920 Hom.: 10371 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.364 AC: 55373 AN: 152038 Hom.: 10383 Cov.: 32 AF XY: 0.364 AC XY: 27056 AN XY: 74286

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.410

Alfa AF: 0.406 Hom.: 27315

Bravo AF: 0.354

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.26

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: rs7762160; hg19: chr6-166015431; COSMIC: COSV64840446;