6-107154308-C-T

Position:

• chr6-107154308-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_020381.4(PDSS2):​c.*311G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.059 in 361,272 control chromosomes in the GnomAD database, including 747 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.056 (262 hom., cov: 33)
  • Exomes 𝑓: 0.061 (485 hom.)
• Consequence: PDSS2 NM_020381.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.405

Genes affected

PDSS2 (HGNC:23041): (decaprenyl diphosphate synthase subunit 2) The protein encoded by this gene is an enzyme that synthesizes the prenyl side-chain of coenzyme Q, or ubiquinone, one of the key elements in the respiratory chain. The gene product catalyzes the formation of all trans-polyprenyl pyrophosphates from isopentyl diphosphate in the assembly of polyisoprenoid side chains, the first step in coenzyme Q biosynthesis. Defects in this gene are a cause of coenzyme Q10 deficiency.[provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BP6: Variant 6-107154308-C-T is Benign according to our data. Variant chr6-107154308-C-T is described in ClinVar as [Benign]. Clinvar id is 1293935.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDSS2	NM_020381.4	c.*311G>A		3_prime_UTR_variant	8/8	ENST00000369037.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDSS2	ENST00000369037.9	c.*311G>A		3_prime_UTR_variant	8/8	1	NM_020381.4	P1

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8462 AN: 152102 Hom.: 262 Cov.: 33

Gnomad AFR AF: 0.0296

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0522

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.0504

GnomAD4 exome AF: 0.0615 AC: 12855 AN: 209052 Hom.: 485 Cov.: 0 AF XY: 0.0570 AC XY: 6512 AN XY: 114252

Gnomad4 AFR exome AF: 0.0305

Gnomad4 AMR exome AF: 0.0512

Gnomad4 ASJ exome AF: 0.0230

Gnomad4 EAS exome AF: 0.000219

Gnomad4 SAS exome AF: 0.0295

Gnomad4 FIN exome AF: 0.0816

Gnomad4 NFE exome AF: 0.0787

Gnomad4 OTH exome AF: 0.0616

GnomAD4 genome AF: 0.0556 AC: 8461 AN: 152220 Hom.: 262 Cov.: 33 AF XY: 0.0551 AC XY: 4099 AN XY: 74428

Gnomad4 AFR AF: 0.0295

Gnomad4 AMR AF: 0.0521

Gnomad4 ASJ AF: 0.0205

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0786

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.0499

Alfa AF: 0.0314 Hom.: 23

Bravo AF: 0.0538

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	14
DANN	Benign	0.87

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: rs41292442; hg19: chr6-107475512;