chr5-60495158-C-A

Variant names:

• chr5-60495158-C-A
• rs26956
• NM_001364599.1:c.-90+981G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001364599.1(PDE4D):​c.-90+981G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,154 control chromosomes in the GnomAD database, including 4,953 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 0.23 (4953 hom., cov: 32)
• Consequence: PDE4D NM_001364599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 13 publications found

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]

ENSG00000305967 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE4D	NM_001364599.1	c.-90+981G>T		intron_variant	Intron 1 of 16		NP_001351528.1
PART1	NR_024617.1	n.711+6735C>A		intron_variant	Intron 1 of 3
PART1	NR_028509.1	n.492+6735C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PART1	ENST00000504876.2	n.217+6735C>A		intron_variant	Intron 1 of 1	2
PDE4D	ENST00000506510.6	n.70+26893G>T		intron_variant	Intron 1 of 2	4
PART1	ENST00000506884.2	n.300+6735C>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35203 AN: 152036 Hom.: 4941 Cov.: 32

Gnomad AFR AF: 0.0744

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.231 AC: 35218 AN: 152154 Hom.: 4953 Cov.: 32 AF XY: 0.236 AC XY: 17590 AN XY: 74394

African (AFR) AF: 0.0742 AC: 3083 AN: 41532

American (AMR) AF: 0.268 AC: 4086 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2009 AN: 5172

South Asian (SAS) AF: 0.449 AC: 2162 AN: 4816

European-Finnish (FIN) AF: 0.272 AC: 2879 AN: 10582

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19554 AN: 67998

Other (OTH) AF: 0.244 AC: 514 AN: 2110

Alfa AF: 0.256 Hom.: 10759

Bravo AF: 0.222

Asia WGS AF: 0.410 AC: 1422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.5
DANN	Benign	0.71
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs26956; hg19: chr5-59790985;