chr5-59769604-T-C

Variant names:

• chr5-59769604-T-C
• rs10940648
• NM_001104631.2:c.455+123564A>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.455+123564A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,212 control chromosomes in the GnomAD database, including 1,959 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 0.14 (1959 hom., cov: 32)
• Consequence: PDE4D NM_001104631.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645
• Publications: 3 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

ENSG00000309959 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 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.455+123564A>G		intron	N/A	NP_001098101.1
	PDE4D	NM_001165899.2		c.272+218884A>G		intron	N/A	NP_001159371.1
	PDE4D	NM_001364599.1		c.272+218884A>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.455+123564A>G		intron	N/A	ENSP00000345502.6
	PDE4D	ENST00000502484.6	TSL:1	c.272+218884A>G		intron	N/A	ENSP00000423094.2
	PDE4D	ENST00000405053.7	TSL:5	n.118+123564A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21272 AN: 152094 Hom.: 1961 Cov.: 32

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.140 AC: 21254 AN: 152212 Hom.: 1959 Cov.: 32 AF XY: 0.136 AC XY: 10147 AN XY: 74418

African (AFR) AF: 0.0389 AC: 1616 AN: 41554

American (AMR) AF: 0.163 AC: 2485 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3466

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0837 AC: 404 AN: 4824

European-Finnish (FIN) AF: 0.161 AC: 1706 AN: 10584

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13441 AN: 67996

Other (OTH) AF: 0.173 AC: 366 AN: 2114

Alfa AF: 0.169 Hom.: 417

Bravo AF: 0.137

Asia WGS AF: 0.0420 AC: 150 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.47
DANN	Benign	0.50
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10940648; hg19: chr5-59065430; COSMIC: COSV58948877; COSMIC: COSV58948877;