NM_001104631.2:c.456-152037A>G

Variant names:

• chr5-59368005-T-C
• rs17782374
• NM_001104631.2:c.456-152037A>G

Variant summary

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

The NM_001104631.2(PDE4D):​c.456-152037A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,246 control chromosomes in the GnomAD database, including 2,510 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 0.17 (2510 hom., cov: 33)
• Consequence: PDE4D NM_001104631.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 7 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]

PDE4D Gene-Disease associations (from GenCC):

• acrodysostosis 2 with or without hormone resistance

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• acrodysostosis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• acrodysostosis with multiple hormone resistance

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• chromosome 5q12 deletion syndrome

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001104631.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDE4D	NM_001104631.2	MANE Select	c.456-152037A>G		intron	N/A	NP_001098101.1
	PDE4D	NM_001165899.2		c.273-152037A>G		intron	N/A	NP_001159371.1
	PDE4D	NM_001364599.1		c.273-152037A>G		intron	N/A	NP_001351528.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDE4D	ENST00000340635.11	TSL:1 MANE Select	c.456-152037A>G		intron	N/A	ENSP00000345502.6
	PDE4D	ENST00000502484.6	TSL:1	c.273-152037A>G		intron	N/A	ENSP00000423094.2
	PDE4D	ENST00000507116.6	TSL:1	c.264-152037A>G		intron	N/A	ENSP00000424852.1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26600 AN: 152128 Hom.: 2511 Cov.: 33

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.175 AC: 26600 AN: 152246 Hom.: 2510 Cov.: 33 AF XY: 0.174 AC XY: 12974 AN XY: 74444

African (AFR) AF: 0.163 AC: 6789 AN: 41554

American (AMR) AF: 0.155 AC: 2365 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 761 AN: 3464

East Asian (EAS) AF: 0.0207 AC: 107 AN: 5178

South Asian (SAS) AF: 0.212 AC: 1022 AN: 4822

European-Finnish (FIN) AF: 0.184 AC: 1950 AN: 10606

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13038 AN: 68006

Other (OTH) AF: 0.164 AC: 346 AN: 2110

Alfa AF: 0.191 Hom.: 5420

Bravo AF: 0.171

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17782374; hg19: chr5-58663831; COSMIC: COSV58947597;