rs16877169

chr5-59481421-C-A

Variant summary

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

The NM_001104631.2(PDE4D):c.456-265453G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 151,822 control chromosomes in the GnomAD database, including 2,994 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 0.16 (2994 hom., cov: 32)
• Consequence: PDE4D NM_001104631.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE4D	NM_001104631.2	c.456-265453G>T		intron_variant		ENST00000340635.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE4D	ENST00000340635.11	c.456-265453G>T		intron_variant		1	NM_001104631.2

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24431 AN: 151706 Hom.: 2987 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0906

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.161 AC: 24454 AN: 151822 Hom.: 2994 Cov.: 32 AF XY: 0.157 AC XY: 11640 AN XY: 74188

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0554

Gnomad4 SAS AF: 0.0598

Gnomad4 FIN AF: 0.0921

Gnomad4 NFE AF: 0.0905

Gnomad4 OTH AF: 0.137

Alfa AF: 0.118 Hom.: 373

Bravo AF: 0.172

Asia WGS AF: 0.0720 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.056
Dann	Benign	0.48

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: rs16877169; hg19: chr5-58777247; COSMIC: COSV58947987;