rs152312

Variant names:

• chr5-60491989-G-A
• rs152312
• NM_001364599.1:c.-90+4150C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-60491989-G-A
• chr5-60491989-G-T

Variant summary

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

The NM_001364599.1(PDE4D):​c.-90+4150C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,122 control chromosomes in the GnomAD database, including 1,339 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 0.11 (1339 hom., cov: 32)
• Consequence: PDE4D NM_001364599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE4D	NM_001364599.1	c.-90+4150C>T		intron_variant	Intron 1 of 16		NP_001351528.1
PDE4D	XM_024446110.2	c.-90+30062C>T		intron_variant	Intron 1 of 17		XP_024301878.1
PDE4D	XM_024446112.2	c.-90+30062C>T		intron_variant	Intron 1 of 16		XP_024301880.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PART1	ENST00000667192.1	n.2755G>A		non_coding_transcript_exon_variant	Exon 2 of 2
PART1	ENST00000504876.2	n.217+3566G>A		intron_variant	Intron 1 of 1	2
PDE4D	ENST00000506510.6	n.70+30062C>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16838 AN: 152004 Hom.: 1325 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.111 AC: 16852 AN: 152122 Hom.: 1339 Cov.: 32 AF XY: 0.114 AC XY: 8512 AN XY: 74374

Gnomad4 AFR AF: 0.0435

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.0770

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0453 Hom.: 36

Bravo AF: 0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs152312; hg19: chr5-59787816;