Variant 1-15807479-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_StrongBP7BS1BS2

The NM_001089591.2(UQCRHL):c.171A>G(p.Val57=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00696 in 1,614,144 control chromosomes in the GnomAD database, including 124 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0064 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0070 ( 116 hom. )

Consequence

UQCRHL
NM_001089591.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.316

Variant links:

Genes affected

UQCRHL (HGNC:51714): (ubiquinol-cytochrome c reductase hinge protein like) This gene has characteristics of a pseudogene derived from the UQCRH gene. However, there is still an open reading frame that could produce a protein of the same or nearly the same size as that of the UQCRH gene, so this gene is being called protein-coding for now. [provided by RefSeq, Jul 2008]

UQCRHL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 1-15807479-T-C is Benign according to our data. Variant chr1-15807479-T-C is described in ClinVar as [Benign]. Clinvar id is 786846.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.316 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00702 (10264/1461886) while in subpopulation MID AF= 0.0472 (272/5768). AF 95% confidence interval is 0.0426. There are 116 homozygotes in gnomad4_exome. There are 5562 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UQCRHL	NM_001089591.2 linkuse as main transcript	c.171A>G	p.Val57=	synonymous_variant	1/1	ENST00000696689.1	NP_001083060.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UQCRHL	ENST00000696689.1 linkuse as main transcript	c.171A>G	p.Val57=	synonymous_variant	1/1		NM_001089591.2	ENSP00000512811	P1
UQCRHL	ENST00000483273.2 linkuse as main transcript	c.171A>G	p.Val57=	synonymous_variant	1/1			ENSP00000485401	P1

Frequencies

GnomAD3 genomes

AF:

0.00637

AC:

969

AN:

152140

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000772

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00604

Gnomad ASJ

AF:

0.0432

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0143

Gnomad FIN

AF:

0.0157

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00632

Gnomad OTH

AF:

0.0110

GnomAD3 exomes

AF:

0.00934

AC:

2348

AN:

251490

Hom.:

AF XY:

0.0105

AC XY:

1427

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.000492

Gnomad AMR exome

AF:

0.00390

Gnomad ASJ exome

AF:

0.0375

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0219

Gnomad FIN exome

AF:

0.0158

Gnomad NFE exome

AF:

0.00665

Gnomad OTH exome

AF:

0.00977

GnomAD4 exome

AF:

0.00702

AC:

10264

AN:

1461886

Hom.:

116

Cov.:

AF XY:

0.00765

AC XY:

5562

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00137

Gnomad4 AMR exome

AF:

0.00429

Gnomad4 ASJ exome

AF:

0.0389

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0204

Gnomad4 FIN exome

AF:

0.0149

Gnomad4 NFE exome

AF:

0.00501

Gnomad4 OTH exome

AF:

0.0102

GnomAD4 genome

AF:

0.00638

AC:

971

AN:

152258

Hom.:

Cov.:

AF XY:

0.00725

AC XY:

540

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.000794

Gnomad4 AMR

AF:

0.00603

Gnomad4 ASJ

AF:

0.0432

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0145

Gnomad4 FIN

AF:

0.0157

Gnomad4 NFE

AF:

0.00632

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.00791

Hom.:

Bravo

AF:

0.00546

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 21, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.2

DANN

Benign

0.71

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