rs2327669

chr6-135894544-C-G

Variant summary

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

The NM_018945.4(PDE7B):c.21+42525C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 151,944 control chromosomes in the GnomAD database, including 39,944 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 0.72 (39944 hom., cov: 31)
• Consequence: PDE7B NM_018945.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925

Genes affected

PDE7B (HGNC:8792): (phosphodiesterase 7B) The 3',5'-cyclic nucleotides cAMP and cGMP function as second messengers in a wide variety of signal transduction pathways. 3',5'-cyclic nucleotide phosphodiesterases (PDEs) catalyze the hydrolysis of cAMP and cGMP to the corresponding 5'-monophosphates and provide a mechanism to downregulate cAMP and cGMP signaling. This gene encodes a cAMP-specific phosphodiesterase, a member of the cyclic nucleotide phosphodiesterase family.[provided by RefSeq, Apr 2009]

LOC101928373 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE7B	NM_018945.4	c.21+42525C>G		intron_variant		ENST00000308191.11
LOC101928373	XR_007059781.1	n.406+26650G>C		intron_variant, non_coding_transcript_variant
LOC101928373	XR_007059780.1	n.488+26650G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE7B	ENST00000308191.11	c.21+42525C>G		intron_variant		1	NM_018945.4	P1

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109113 AN: 151826 Hom.: 39886 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.719 AC: 109231 AN: 151944 Hom.: 39944 Cov.: 31 AF XY: 0.720 AC XY: 53430 AN XY: 74234

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.695

Alfa AF: 0.695 Hom.: 4592

Bravo AF: 0.727

Asia WGS AF: 0.766 AC: 2666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.5
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2327669; hg19: chr6-136215682;