Variant chr20-35384111-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018244.5(UQCC1):c.152G>A(p.Arg51Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 1,610,670 control chromosomes in the GnomAD database, including 297,383 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.54 ( 23427 hom., cov: 32)

Exomes 𝑓: 0.61 ( 273956 hom. )

Consequence

UQCC1
NM_018244.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.150

Variant links:

Genes affected

UQCC1 (HGNC:15891): (ubiquinol-cytochrome c reductase complex assembly factor 1) This gene encodes a transmembrane protein that is structurally similar to the mouse basic fibroblast growth factor repressed ZIC-binding protein. In mouse this protein may be involved in fibroblast growth factor regulated growth control. In humans, polymorphisms in this gene are associated with variation in human height and osteoarthritis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

UQCC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.5950916E-6).

BP6

Variant 20-35384111-C-T is Benign according to our data. Variant chr20-35384111-C-T is described in ClinVar as [Benign]. Clinvar id is 1245347.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UQCC1	NM_018244.5 link	c.152G>A	p.Arg51Gln	missense_variant	3/10	ENST00000374385.10	NP_060714.3	Q9NVA1-1Q3KRB6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UQCC1	ENST00000374385.10 link	c.152G>A	p.Arg51Gln	missense_variant	3/10	1	NM_018244.5	ENSP00000363506.5		Q9NVA1-1

Frequencies

GnomAD3 genomes

AF:

0.543

AC:

82488

AN:

151866

Hom.:

23421

Cov.:

show subpopulations

Gnomad AFR

AF:

0.366

Gnomad AMI

AF:

0.610

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.556

Gnomad EAS

AF:

0.717

Gnomad SAS

AF:

0.444

Gnomad FIN

AF:

0.572

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.615

Gnomad OTH

AF:

0.565

GnomAD3 exomes

AF:

0.589

AC:

147843

AN:

251060

Hom.:

45023

AF XY:

0.581

AC XY:

78812

AN XY:

135714

show subpopulations

Gnomad AFR exome

AF:

0.354

Gnomad AMR exome

AF:

0.741

Gnomad ASJ exome

AF:

0.550

Gnomad EAS exome

AF:

0.713

Gnomad SAS exome

AF:

0.439

Gnomad FIN exome

AF:

0.574

Gnomad NFE exome

AF:

0.603

Gnomad OTH exome

AF:

0.581

GnomAD4 exome

AF:

0.608

AC:

887318

AN:

1458686

Hom.:

273956

Cov.:

AF XY:

0.603

AC XY:

437287

AN XY:

725732

show subpopulations

Gnomad4 AFR exome

AF:

0.352

Gnomad4 AMR exome

AF:

0.730

Gnomad4 ASJ exome

AF:

0.557

Gnomad4 EAS exome

AF:

0.741

Gnomad4 SAS exome

AF:

0.441

Gnomad4 FIN exome

AF:

0.575

Gnomad4 NFE exome

AF:

0.623

Gnomad4 OTH exome

AF:

0.594

GnomAD4 genome

AF:

0.543

AC:

82499

AN:

151984

Hom.:

23427

Cov.:

AF XY:

0.541

AC XY:

40227

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.365

Gnomad4 AMR

AF:

0.649

Gnomad4 ASJ

AF:

0.556

Gnomad4 EAS

AF:

0.717

Gnomad4 SAS

AF:

0.443

Gnomad4 FIN

AF:

0.572

Gnomad4 NFE

AF:

0.615

Gnomad4 OTH

AF:

0.558

Alfa

AF:

0.598

Hom.:

71108

Bravo

AF:

0.548

TwinsUK

AF:

0.620

AC:

2298

ALSPAC

AF:

0.633

AC:

2439

ESP6500AA

AF:

0.366

AC:

1612

ESP6500EA

AF:

0.608

AC:

5226

ExAC

AF:

0.577

AC:

70058

Asia WGS

AF:

0.483

AC:

1681

AN:

3478

EpiCase

AF:

0.612

EpiControl

AF:

0.601

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 18, 2020	This variant is associated with the following publications: (PMID: 19343178) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.067

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.63

CADD

Benign

0.30

DANN

Benign

0.62

DEOGEN2

Benign

0.017

.;T;.;T;T;T;.

Eigen

Benign

-1.9

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.0097

LIST_S2

Benign

0.33

T;T;T;T;T;T;T

MetaRNN

Benign

0.0000016

T;T;T;T;T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-0.60

N;.;N;N;.;.;.

PrimateAI

Benign

0.19

PROVEAN

Benign

-0.84

N;N;N;N;.;N;N

REVEL

Benign

0.024

Sift

Benign

0.42

T;T;T;T;.;T;T

Sift4G

Benign

0.39

T;T;T;T;T;.;T

Polyphen

0.0, 0.022

.;.;.;B;.;.;B

Vest4

0.024

MPC

0.33

ClinPred

0.028

GERP RS

-9.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.012

gMVP

0.17

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over