rs487278

Variant names:

• chr6-136180690-G-A
• rs487278
• NM_018945.4:c.949-537G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-136180690-G-A
• chr6-136180690-G-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.949-537G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,156 control chromosomes in the GnomAD database, including 20,970 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 0.49 (20970 hom., cov: 33)
• Consequence: PDE7B NM_018945.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018945.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDE7B	NM_018945.4	MANE Select	c.949-537G>A		intron	N/A	NP_061818.1	Q9NP56

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDE7B	ENST00000308191.11	TSL:1 MANE Select	c.949-537G>A		intron	N/A	ENSP00000310661.6	Q9NP56
	PDE7B	ENST00000615259.4	TSL:1	c.1105-537G>A		intron	N/A	ENSP00000482117.1	A1E5M1
	PDE7B-AS1	ENST00000417643.5	TSL:5	n.59-18342C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74575 AN: 152038 Hom.: 20982 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.490 AC: 74560 AN: 152156 Hom.: 20970 Cov.: 33 AF XY: 0.494 AC XY: 36717 AN XY: 74382

African (AFR) AF: 0.194 AC: 8062 AN: 41530

American (AMR) AF: 0.515 AC: 7872 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2245 AN: 3472

East Asian (EAS) AF: 0.591 AC: 3060 AN: 5178

South Asian (SAS) AF: 0.687 AC: 3316 AN: 4826

European-Finnish (FIN) AF: 0.545 AC: 5761 AN: 10568

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42477 AN: 67982

Other (OTH) AF: 0.512 AC: 1081 AN: 2112

Alfa AF: 0.573 Hom.: 39998

Bravo AF: 0.473

Asia WGS AF: 0.585 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.90
DANN	Benign	0.33
PhyloP100		-0.34
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: rs487278; hg19: chr6-136501828;