rs16878206

Variant names:

• chr5-60520967-A-G
• rs16878206
• XM_024446110.2:c.-90+1084T>C

Variant summary

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

The XM_024446110.2(PDE4D):​c.-90+1084T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,342 control chromosomes in the GnomAD database, including 15,536 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 0.38 (15523 hom., cov: 32)
  • Exomes 𝑓: 0.24 (13 hom.)
• Consequence: PDE4D XM_024446110.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

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]

PART1 (HGNC:17263): (prostate androgen-regulated transcript 1) This gene is induced by androgen in prostate adenocarcinoma cells. Multiple alternatively transcript variants have been described for this gene, none of which are predicted to encode a protein product. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE4D	XM_024446110.2	c.-90+1084T>C		intron_variant	Intron 1 of 17		XP_024301878.1
PDE4D	XM_024446112.2	c.-90+1084T>C		intron_variant	Intron 1 of 16		XP_024301880.1
PART1	NR_024617.1	n.712-8437A>G		intron_variant	Intron 1 of 3
PART1	NR_028509.1	n.493-53A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PART1	ENST00000504876.2	n.218-53A>G		intron_variant	Intron 1 of 1	2
PDE4D	ENST00000506510.6	n.70+1084T>C		intron_variant	Intron 1 of 2	4
PART1	ENST00000506884.2	n.301-8437A>G		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58177 AN: 151922 Hom.: 15469 Cov.: 32

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0194

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.350

GnomAD4 exome AF: 0.238 AC: 72 AN: 302 Hom.: 13 AF XY: 0.190 AC XY: 40 AN XY: 210

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.341

Gnomad4 NFE exome AF: 0.201

Gnomad4 OTH exome AF: 0.0714

GnomAD4 genome AF: 0.383 AC: 58285 AN: 152040 Hom.: 15523 Cov.: 32 AF XY: 0.375 AC XY: 27862 AN XY: 74302

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.347

Alfa AF: 0.346 Hom.: 1471

Bravo AF: 0.397

Asia WGS AF: 0.150 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.068
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16878206; hg19: chr5-59816794;