chr6-135921170-G-A

Position:

• chr6-135921170-G-A

Variant summary

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

The NM_018945.4(PDE7B):​c.22-26294G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,104 control chromosomes in the GnomAD database, including 1,724 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 0.14 (1724 hom., cov: 32)
• Consequence: PDE7B NM_018945.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

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]

LOC101928373 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDE7B	NM_018945.4	c.22-26294G>A		intron_variant		ENST00000308191.11
LOC101928373	XR_007059781.1	n.406+24C>T		intron_variant, non_coding_transcript_variant
LOC101928373	XR_007059780.1	n.488+24C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDE7B	ENST00000308191.11	c.22-26294G>A		intron_variant		1	NM_018945.4	P1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20927 AN: 151986 Hom.: 1721 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.138 AC: 20954 AN: 152104 Hom.: 1724 Cov.: 32 AF XY: 0.140 AC XY: 10386 AN XY: 74334

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.0553

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.132

Alfa AF: 0.130 Hom.: 218

Bravo AF: 0.147

Asia WGS AF: 0.307 AC: 1069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	7.4
DANN	Benign	0.61

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: rs9376165; hg19: chr6-136242308;