rs9389370

Variant names:

• chr6-136110127-C-G
• rs9389370
• NM_018945.4:c.166+1313C>G

Variant summary

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

The NM_018945.4(PDE7B):​c.166+1313C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,934 control chromosomes in the GnomAD database, including 7,414 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 0.28 (7414 hom., cov: 31)
• Consequence: PDE7B NM_018945.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 6 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE7B	NM_018945.4	c.166+1313C>G		intron_variant	Intron 3 of 12	ENST00000308191.11	NP_061818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE7B	ENST00000308191.11	c.166+1313C>G		intron_variant	Intron 3 of 12	1	NM_018945.4	ENSP00000310661.6

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42694 AN: 151816 Hom.: 7417 Cov.: 31

Gnomad AFR AF: 0.0650

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.281 AC: 42693 AN: 151934 Hom.: 7414 Cov.: 31 AF XY: 0.285 AC XY: 21188 AN XY: 74244

African (AFR) AF: 0.0649 AC: 2692 AN: 41464

American (AMR) AF: 0.287 AC: 4388 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3472

East Asian (EAS) AF: 0.333 AC: 1721 AN: 5162

South Asian (SAS) AF: 0.438 AC: 2105 AN: 4808

European-Finnish (FIN) AF: 0.420 AC: 4414 AN: 10508

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.371 AC: 25203 AN: 67934

Other (OTH) AF: 0.295 AC: 623 AN: 2110

Alfa AF: 0.329 Hom.: 1135

Bravo AF: 0.257

Asia WGS AF: 0.376 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.5
DANN	Benign	0.77
PhyloP100		-0.0040
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9389370; hg19: chr6-136431265;