6-136032167-C-T

Variant names:

• chr6-136032167-C-T
• rs11154849
• NM_018945.4:c.83-76564C>T

Variant summary

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

The NM_018945.4(PDE7B):​c.83-76564C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,046 control chromosomes in the GnomAD database, including 8,775 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 0.33 (8775 hom., cov: 32)
• Consequence: PDE7B NM_018945.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.32
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE7B	NM_018945.4	c.83-76564C>T		intron_variant	Intron 2 of 12	ENST00000308191.11	NP_061818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE7B	ENST00000308191.11	c.83-76564C>T		intron_variant	Intron 2 of 12	1	NM_018945.4	ENSP00000310661.6
PDE7B-AS1	ENST00000626414.1	n.74-19454G>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50436 AN: 151928 Hom.: 8757 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.332 AC: 50487 AN: 152046 Hom.: 8775 Cov.: 32 AF XY: 0.337 AC XY: 25014 AN XY: 74314

African (AFR) AF: 0.222 AC: 9195 AN: 41470

American (AMR) AF: 0.430 AC: 6573 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1234 AN: 3466

East Asian (EAS) AF: 0.419 AC: 2163 AN: 5162

South Asian (SAS) AF: 0.335 AC: 1612 AN: 4818

European-Finnish (FIN) AF: 0.363 AC: 3836 AN: 10558

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.362 AC: 24583 AN: 67980

Other (OTH) AF: 0.368 AC: 775 AN: 2108

Alfa AF: 0.333 Hom.: 1082

Bravo AF: 0.336

Asia WGS AF: 0.401 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.047
DANN	Benign	0.59
PhyloP100		-3.3
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: rs11154849; hg19: chr6-136353305;