chr6-107194186-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020381.4(PDSS2):​c.1009-332G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,086 control chromosomes in the GnomAD database, including 5,130 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 0.23 ( 5130 hom., cov: 32)

Consequence

PDSS2
NM_020381.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0640
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PDSS2NM_020381.4 linkc.1009-332G>A intron_variant Intron 6 of 7 ENST00000369037.9 NP_065114.3 Q86YH6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PDSS2ENST00000369037.9 linkc.1009-332G>A intron_variant Intron 6 of 7 1 NM_020381.4 ENSP00000358033.4 Q86YH6-1

Frequencies

GnomAD3 genomes
AF:
0.234
AC:
35596
AN:
151966
Hom.:
5119
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0665
Gnomad AMI
AF:
0.464
Gnomad AMR
AF:
0.328
Gnomad ASJ
AF:
0.322
Gnomad EAS
AF:
0.488
Gnomad SAS
AF:
0.323
Gnomad FIN
AF:
0.282
Gnomad MID
AF:
0.231
Gnomad NFE
AF:
0.274
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.234
AC:
35621
AN:
152086
Hom.:
5130
Cov.:
32
AF XY:
0.239
AC XY:
17754
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.0665
Gnomad4 AMR
AF:
0.328
Gnomad4 ASJ
AF:
0.322
Gnomad4 EAS
AF:
0.487
Gnomad4 SAS
AF:
0.324
Gnomad4 FIN
AF:
0.282
Gnomad4 NFE
AF:
0.274
Gnomad4 OTH
AF:
0.263
Alfa
AF:
0.177
Hom.:
529
Bravo
AF:
0.232
Asia WGS
AF:
0.390
AC:
1355
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
3.5
DANN
Benign
0.82

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3734679; hg19: chr6-107515390; API