6-165633546-A-G

Position:

• chr6-165633546-A-G

Variant summary

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

The NM_001385079.1(PDE10A):​c.865+28401T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,094 control chromosomes in the GnomAD database, including 7,875 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 0.32 (7875 hom., cov: 33)
• Consequence: PDE10A NM_001385079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

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 (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE10A	NM_001385079.1	c.865+28401T>C		intron_variant		ENST00000539869.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE10A	ENST00000539869.4	c.865+28401T>C		intron_variant		1	NM_001385079.1	P3

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48252 AN: 151976 Hom.: 7865 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.317 AC: 48283 AN: 152094 Hom.: 7875 Cov.: 33 AF XY: 0.316 AC XY: 23485 AN XY: 74348

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.333

Alfa AF: 0.308 Hom.: 933

Bravo AF: 0.318

Asia WGS AF: 0.277 AC: 960 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	1.2
DANN	Benign	0.30

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: rs1079418; hg19: chr6-166047034;