chr17-81650906-TC-T

Position:

• chr17-81650906-TC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002602.4(PDE6G):​c.*167delG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0464 in 686,428 control chromosomes in the GnomAD database, including 1,638 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.042 (250 hom., cov: 32)
  • Exomes 𝑓: 0.048 (1388 hom.)
• Consequence: PDE6G NM_002602.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.558

Genes affected

PDE6G (HGNC:8789): (phosphodiesterase 6G) This gene encodes the gamma subunit of cyclic GMP-phosphodiesterase, which is composed of alpha- and beta- catalytic subunits and two identical, inhibitory gamma subunits. This gene is expressed in rod photoreceptors and functions in the phototransduction signaling cascade. It is also expressed in a variety of other tissues, and has been shown to regulate the c-Src protein kinase and G-protein-coupled receptor kinase 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2009]

PDE6G (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-81650906-TC-T is Benign according to our data. Variant chr17-81650906-TC-T is described in ClinVar as [Likely_benign]. Clinvar id is 325859.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDE6G	NM_002602.4	c.*167delG		3_prime_UTR_variant	4/4	ENST00000331056.10	NP_002593.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDE6G	ENST00000331056.10	c.*167delG		3_prime_UTR_variant	4/4	1	NM_002602.4	ENSP00000328412.5
PDE6G	ENST00000574024.1	n.364delG		non_coding_transcript_exon_variant	3/3	1
PDE6G	ENST00000574777.1	n.331delG		non_coding_transcript_exon_variant	3/3	2
PDE6G	ENST00000571224.5	c.*167delG		downstream_gene_variant		5		ENSP00000458167.1

Frequencies

GnomAD3 genomes AF: 0.0424 AC: 6436 AN: 151962 Hom.: 249 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.0637

Gnomad FIN AF: 0.0116

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0312

GnomAD3 exomes AF: 0.0484 AC: 6924 AN: 142938 Hom.: 385 AF XY: 0.0485 AC XY: 3714 AN XY: 76648

Gnomad AFR exome AF: 0.0443

Gnomad AMR exome AF: 0.0235

Gnomad ASJ exome AF: 0.0191

Gnomad EAS exome AF: 0.212

Gnomad SAS exome AF: 0.0564

Gnomad FIN exome AF: 0.0135

Gnomad NFE exome AF: 0.0350

Gnomad OTH exome AF: 0.0386

GnomAD4 exome AF: 0.0476 AC: 25427 AN: 534348 Hom.: 1388 Cov.: 4 AF XY: 0.0474 AC XY: 13729 AN XY: 289382

Gnomad4 AFR exome AF: 0.0443

Gnomad4 AMR exome AF: 0.0246

Gnomad4 ASJ exome AF: 0.0193

Gnomad4 EAS exome AF: 0.249

Gnomad4 SAS exome AF: 0.0566

Gnomad4 FIN exome AF: 0.0138

Gnomad4 NFE exome AF: 0.0347

Gnomad4 OTH exome AF: 0.0462

GnomAD4 genome AF: 0.0424 AC: 6445 AN: 152080 Hom.: 250 Cov.: 32 AF XY: 0.0417 AC XY: 3100 AN XY: 74330

Gnomad4 AFR AF: 0.0437

Gnomad4 AMR AF: 0.0368

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.0637

Gnomad4 FIN AF: 0.0116

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.0321 Hom.: 20

Bravo AF: 0.0451

Asia WGS AF: 0.131 AC: 455 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Retinitis Pigmentosa, Recessive Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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: rs58894371; hg19: chr17-79617936;