chr6-136160253-A-G

Variant names:

• chr6-136160253-A-G
• rs509342
• NM_018945.4:c.711+4495A>G

Variant summary

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

The ENST00000308191.11(PDE7B):​c.711+4495A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,066 control chromosomes in the GnomAD database, including 42,743 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 0.74 (42743 hom., cov: 31)
• Consequence: PDE7B ENST00000308191.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000308191.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDE7B	NM_018945.4	MANE Select	c.711+4495A>G		intron	N/A	NP_061818.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDE7B	ENST00000308191.11	TSL:1 MANE Select	c.711+4495A>G		intron	N/A	ENSP00000310661.6
	PDE7B	ENST00000615259.4	TSL:1	c.867+4495A>G		intron	N/A	ENSP00000482117.1
	PDE7B-AS1	ENST00000417643.5	TSL:5	n.155+1999T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112160 AN: 151948 Hom.: 42690 Cov.: 31

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.738 AC: 112275 AN: 152066 Hom.: 42743 Cov.: 31 AF XY: 0.738 AC XY: 54838 AN XY: 74328

African (AFR) AF: 0.938 AC: 38952 AN: 41522

American (AMR) AF: 0.739 AC: 11291 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2406 AN: 3472

East Asian (EAS) AF: 0.707 AC: 3631 AN: 5136

South Asian (SAS) AF: 0.748 AC: 3598 AN: 4812

European-Finnish (FIN) AF: 0.606 AC: 6416 AN: 10580

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43713 AN: 67954

Other (OTH) AF: 0.735 AC: 1552 AN: 2112

Alfa AF: 0.690 Hom.: 61721

Bravo AF: 0.757

Asia WGS AF: 0.772 AC: 2686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.32
PhyloP100		0.0070
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: rs509342; hg19: chr6-136481391;