5-77426617-C-T

Variant names:

• chr5-77426617-C-T
• rs62362531
• NM_003719.5:c.*63C>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003719.5(PDE8B):​c.*63C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 852,860 control chromosomes in the GnomAD database, including 9,460 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.11 (1228 hom., cov: 32)
  • Exomes 𝑓: 0.15 (8232 hom.)
• Consequence: PDE8B NM_003719.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.559

Genes affected

PDE8B (HGNC:8794): (phosphodiesterase 8B) The protein encoded by this gene is a cyclic nucleotide phosphodiesterase (PDE) that catalyzes the hydrolysis of the second messenger cAMP. The encoded protein, which does not hydrolyze cGMP, is resistant to several PDE inhibitors. Defects in this gene are a cause of autosomal dominant striatal degeneration (ADSD). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2010]

ENSG00000284762 (HGNC:):

WDR41 (HGNC:25601): (WD repeat domain 41) Contributes to guanyl-nucleotide exchange factor activity. Involved in regulation of autophagy. Located in cytoplasm. Part of guanyl-nucleotide exchange factor complex. Colocalizes with Atg1/ULK1 kinase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 5-77426617-C-T is Benign according to our data. Variant chr5-77426617-C-T is described in ClinVar as [Benign]. Clinvar id is 354178.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDE8B	NM_003719.5	c.*63C>T		3_prime_UTR_variant	Exon 22 of 22	ENST00000264917.10	NP_003710.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDE8B	ENST00000264917.10	c.*63C>T		3_prime_UTR_variant	Exon 22 of 22	1	NM_003719.5	ENSP00000264917.6
ENSG00000284762	ENST00000646262.1	c.*63C>T		3_prime_UTR_variant	Exon 24 of 24			ENSP00000493971.1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17291 AN: 152158 Hom.: 1226 Cov.: 32

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.110

GnomAD4 exome AF: 0.146 AC: 102098 AN: 700582 Hom.: 8232 Cov.: 9 AF XY: 0.147 AC XY: 55119 AN XY: 374176

Gnomad4 AFR exome AF: 0.0276

Gnomad4 AMR exome AF: 0.0752

Gnomad4 ASJ exome AF: 0.0573

Gnomad4 EAS exome AF: 0.118

Gnomad4 SAS exome AF: 0.169

Gnomad4 FIN exome AF: 0.161

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.132

GnomAD4 genome AF: 0.114 AC: 17299 AN: 152278 Hom.: 1228 Cov.: 32 AF XY: 0.113 AC XY: 8434 AN XY: 74442

Gnomad4 AFR AF: 0.0303

Gnomad4 AMR AF: 0.0976

Gnomad4 ASJ AF: 0.0562

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.113

Alfa AF: 0.112 Hom.: 168

Bravo AF: 0.102

Asia WGS AF: 0.155 AC: 539 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Striatal Degeneration Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal dominant striatal neurodegeneration type 1 Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.6
DANN	Benign	0.78

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: rs62362531; hg19: chr5-76722442; COSMIC: COSV53732071; COSMIC: COSV53732071;