Variant chr19-29213095-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006003.3(UQCRFS1):c.24A>G(p.Ser8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.93 in 152,110 control chromosomes in the GnomAD database, including 65,752 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.93 ( 65752 hom., cov: 37)

Exomes 𝑓: 0.92 ( 579285 hom. )

Failed GnomAD Quality Control

Consequence

UQCRFS1
NM_006003.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.645

Variant links:

Genes affected

UQCRFS1 (HGNC:12587): (ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1) Predicted to enable oxidoreductase activity. Involved in mitochondrial respiratory chain complex III assembly and respiratory electron transport chain. Located in mitochondrion. Part of mitochondrial respiratory chain complex III and mitochondrial respiratory chain complex IV. Implicated in mitochondrial complex III deficiency. [provided by Alliance of Genome Resources, Apr 2022]

UQCRFS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 19-29213095-T-C is Benign according to our data. Variant chr19-29213095-T-C is described in ClinVar as [Benign]. Clinvar id is 1684191.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.645 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UQCRFS1	NM_006003.3 linkuse as main transcript	c.24A>G	p.Ser8=	synonymous_variant	1/2	ENST00000304863.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCRFS1	ENST00000304863.6 linkuse as main transcript	c.24A>G	p.Ser8=	synonymous_variant	1/2	1	NM_006003.3	P1

Frequencies

GnomAD3 genomes

AF:

0.930

AC:

141304

AN:

152000

Hom.:

65700

Cov.:

show subpopulations

Gnomad AFR

AF:

0.935

Gnomad AMI

AF:

0.891

Gnomad AMR

AF:

0.929

Gnomad ASJ

AF:

0.910

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.967

Gnomad FIN

AF:

0.939

Gnomad MID

AF:

0.924

Gnomad NFE

AF:

0.919

Gnomad OTH

AF:

0.922

GnomAD3 exomes

AF:

0.932

AC:

95447

AN:

102368

Hom.:

44584

AF XY:

0.933

AC XY:

53644

AN XY:

57472

show subpopulations

Gnomad AFR exome

AF:

0.880

Gnomad AMR exome

AF:

0.945

Gnomad ASJ exome

AF:

0.907

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.954

Gnomad FIN exome

AF:

0.936

Gnomad NFE exome

AF:

0.910

Gnomad OTH exome

AF:

0.913

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.924

AC:

1252892

AN:

1355800

Hom.:

579285

Cov.:

AF XY:

0.925

AC XY:

618591

AN XY:

669030

show subpopulations

Gnomad4 AFR exome

AF:

0.935

Gnomad4 AMR exome

AF:

0.942

Gnomad4 ASJ exome

AF:

0.910

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.955

Gnomad4 FIN exome

AF:

0.931

Gnomad4 NFE exome

AF:

0.919

Gnomad4 OTH exome

AF:

0.925

GnomAD4 genome

AF:

0.930

AC:

141411

AN:

152110

Hom.:

65752

Cov.:

AF XY:

0.931

AC XY:

69251

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.935

Gnomad4 AMR

AF:

0.929

Gnomad4 ASJ

AF:

0.910

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.966

Gnomad4 FIN

AF:

0.939

Gnomad4 NFE

AF:

0.919

Gnomad4 OTH

AF:

0.924

Alfa

AF:

0.913

Hom.:

5897

Bravo

AF:

0.928

Asia WGS

AF:

0.981

AC:

3413

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Mitochondrial complex 3 deficiency, nuclear type 10

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

8.8

DANN

Benign

0.46

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

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