rs10940648

Positions:

• chr5-59769604-T-C

Variant summary

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

The NM_001104631.2(PDE4D):​c.455+123564A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,212 control chromosomes in the GnomAD database, including 1,959 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 0.14 (1959 hom., cov: 32)
• Consequence: PDE4D NM_001104631.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645

Genes affected

PDE4D (HGNC:8783): (phosphodiesterase 4D) This gene encodes one of four mammalian counterparts to the fruit fly 'dunce' gene. The encoded protein has 3',5'-cyclic-AMP phosphodiesterase activity and degrades cAMP, which acts as a signal transduction molecule in multiple cell types. This gene uses different promoters to generate multiple alternatively spliced transcript variants that encode functional proteins.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE4D	NM_001104631.2	c.455+123564A>G		intron_variant		ENST00000340635.11	NP_001098101.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE4D	ENST00000340635.11	c.455+123564A>G		intron_variant		1	NM_001104631.2	ENSP00000345502

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21272 AN: 152094 Hom.: 1961 Cov.: 32

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.140 AC: 21254 AN: 152212 Hom.: 1959 Cov.: 32 AF XY: 0.136 AC XY: 10147 AN XY: 74418

Gnomad4 AFR AF: 0.0389

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0837

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.173

Alfa AF: 0.169 Hom.: 417

Bravo AF: 0.137

Asia WGS AF: 0.0420 AC: 150 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.47
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10940648; hg19: chr5-59065430; COSMIC: COSV58948877; COSMIC: COSV58948877;