Variant 19-29207902-G-A 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.471C>T(p.Ser157=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00307 in 1,613,898 control chromosomes in the GnomAD database, including 111 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0033 ( 11 hom., cov: 33)

Exomes 𝑓: 0.0030 ( 100 hom. )

Consequence

UQCRFS1
NM_006003.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.55

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=-0.89).

BP6

Variant 19-29207902-G-A is Benign according to our data. Variant chr19-29207902-G-A is described in ClinVar as [Benign]. Clinvar id is 789459.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.55 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0602 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.471C>T	p.Ser157=	synonymous_variant	2/2	ENST00000304863.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCRFS1	ENST00000304863.6 linkuse as main transcript	c.471C>T	p.Ser157=	synonymous_variant	2/2	1	NM_006003.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00331

AC:

504

AN:

152130

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0102

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0495

Gnomad SAS

AF:

0.00518

Gnomad FIN

AF:

0.00330

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000294

Gnomad OTH

AF:

0.000960

GnomAD3 exomes

AF:

0.00910

AC:

2279

AN:

250486

Hom.:

AF XY:

0.00766

AC XY:

1038

AN XY:

135496

show subpopulations

Gnomad AFR exome

AF:

0.0000628

Gnomad AMR exome

AF:

0.0325

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0535

Gnomad SAS exome

AF:

0.00134

Gnomad FIN exome

AF:

0.00347

Gnomad NFE exome

AF:

0.000221

Gnomad OTH exome

AF:

0.00475

GnomAD4 exome

AF:

0.00305

AC:

4457

AN:

1461650

Hom.:

100

Cov.:

AF XY:

0.00286

AC XY:

2083

AN XY:

727134

show subpopulations

Gnomad4 AFR exome

AF:

0.000179

Gnomad4 AMR exome

AF:

0.0295

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0622

Gnomad4 SAS exome

AF:

0.00167

Gnomad4 FIN exome

AF:

0.00359

Gnomad4 NFE exome

AF:

0.000154

Gnomad4 OTH exome

AF:

0.00238

GnomAD4 genome

AF:

0.00332

AC:

505

AN:

152248

Hom.:

Cov.:

AF XY:

0.00371

AC XY:

276

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.000241

Gnomad4 AMR

AF:

0.0102

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0496

Gnomad4 SAS

AF:

0.00519

Gnomad4 FIN

AF:

0.00330

Gnomad4 NFE

AF:

0.000294

Gnomad4 OTH

AF:

0.000950

Alfa

AF:

0.00109

Hom.:

Bravo

AF:

0.00491

EpiCase

AF:

0.000109

EpiControl

AF:

0.00

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	Labcorp Genetics (formerly Invitae), Labcorp	May 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.26

DANN

Benign

0.54

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