rs11154851

Positions:

• chr6-136046867-C-T

Variant summary

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

The NM_018945.4(PDE7B):​c.83-61864C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.067 in 152,120 control chromosomes in the GnomAD database, including 436 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 0.067 (436 hom., cov: 32)
• Consequence: PDE7B NM_018945.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE7B	NM_018945.4	c.83-61864C>T		intron_variant		ENST00000308191.11	NP_061818.1
PDE7B-AS1	NR_149042.1	n.489-1934G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE7B	ENST00000308191.11	c.83-61864C>T		intron_variant		1	NM_018945.4	ENSP00000310661.6

Frequencies

GnomAD3 genomes AF: 0.0669 AC: 10165 AN: 152002 Hom.: 433 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0931

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.0755

Gnomad SAS AF: 0.0388

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0365

Gnomad OTH AF: 0.0618

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

GnomAD4 genome AF: 0.0670 AC: 10189 AN: 152120 Hom.: 436 Cov.: 32 AF XY: 0.0688 AC XY: 5114 AN XY: 74366

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0934

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.0759

Gnomad4 SAS AF: 0.0387

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.0365

Gnomad4 OTH AF: 0.0626

Alfa AF: 0.0449 Hom.: 201

Bravo AF: 0.0718

Asia WGS AF: 0.0650 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.41

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: rs11154851; hg19: chr6-136368005;