chr6-136160474-G-T

Position:

• chr6-136160474-G-T

Variant summary

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

The NM_018945.4(PDE7B):​c.711+4716G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,048 control chromosomes in the GnomAD database, including 12,047 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 0.24 (12047 hom., cov: 32)
• Consequence: PDE7B NM_018945.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE7B	NM_018945.4	c.711+4716G>T		intron_variant		ENST00000308191.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE7B	ENST00000308191.11	c.711+4716G>T		intron_variant		1	NM_018945.4	P1
PDE7B-AS1	ENST00000655618.1	n.178+1778C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36331 AN: 151930 Hom.: 11992 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0625

Gnomad FIN AF: 0.0572

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.00797

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.240 AC: 36461 AN: 152048 Hom.: 12047 Cov.: 32 AF XY: 0.236 AC XY: 17562 AN XY: 74346

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0623

Gnomad4 FIN AF: 0.0572

Gnomad4 NFE AF: 0.00797

Gnomad4 OTH AF: 0.214

Alfa AF: 0.164 Hom.: 1144

Bravo AF: 0.277

Asia WGS AF: 0.172 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.30
DANN	Benign	0.59

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: rs9321552; hg19: chr6-136481612;