rs560713

chr6-136183898-A-Cchr6-136183898-A-Gchr6-136183898-A-T

Variant summary

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

The NM_018945.4(PDE7B):c.1045+2575A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 151,974 control chromosomes in the GnomAD database, including 45,039 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 0.76 (45039 hom., cov: 30)
• Consequence: PDE7B NM_018945.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

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]

PDE7B-AS1 (HGNC:56334): (PDE7B antisense RNA 1)

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 (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE7B	NM_018945.4	c.1045+2575A>C		intron_variant		ENST00000308191.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE7B	ENST00000308191.11	c.1045+2575A>C		intron_variant		1	NM_018945.4	P1
PDE7B-AS1	ENST00000655618.1	n.82-21550T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115500 AN: 151858 Hom.: 44986 Cov.: 30

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.761 AC: 115614 AN: 151974 Hom.: 45039 Cov.: 30 AF XY: 0.763 AC XY: 56686 AN XY: 74266

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.755

Alfa AF: 0.678 Hom.: 16817

Bravo AF: 0.772

Asia WGS AF: 0.810 AC: 2817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.2
Dann	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs560713; hg19: chr6-136505036;