Variant chr1-15807492-T-C 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_001089591.2(UQCRHL):c.158A>G(p.Tyr53Cys) variant causes a missense change. The variant allele was found at a frequency of 0.124 in 1,613,884 control chromosomes in the GnomAD database, including 15,100 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 3218 hom., cov: 31)

Exomes 𝑓: 0.12 ( 11882 hom. )

Consequence

UQCRHL
NM_001089591.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.66

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005833328).

BP6

Variant 1-15807492-T-C is Benign according to our data. Variant chr1-15807492-T-C is described in ClinVar as [Benign]. Clinvar id is 767656.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UQCRHL	NM_001089591.2 linkuse as main transcript	c.158A>G	p.Tyr53Cys	missense_variant	1/1	ENST00000696689.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCRHL	ENST00000696689.1 linkuse as main transcript	c.158A>G	p.Tyr53Cys	missense_variant	1/1		NM_001089591.2	P1
UQCRHL	ENST00000483273.2 linkuse as main transcript	c.158A>G	p.Tyr53Cys	missense_variant	1/1			P1

Frequencies

GnomAD3 genomes

AF:

0.175

AC:

26594

AN:

151934

Hom.:

3210

Cov.:

show subpopulations

Gnomad AFR

AF:

0.333

Gnomad AMI

AF:

0.0658

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.00540

Gnomad SAS

AF:

0.0729

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.143

GnomAD3 exomes

AF:

0.118

AC:

29681

AN:

251462

Hom.:

2473

AF XY:

0.115

AC XY:

15641

AN XY:

135914

show subpopulations

Gnomad AFR exome

AF:

0.337

Gnomad AMR exome

AF:

0.0637

Gnomad ASJ exome

AF:

0.125

Gnomad EAS exome

AF:

0.00228

Gnomad SAS exome

AF:

0.0876

Gnomad FIN exome

AF:

0.182

Gnomad NFE exome

AF:

0.117

Gnomad OTH exome

AF:

0.119

GnomAD4 exome

AF:

0.119

AC:

173757

AN:

1461832

Hom.:

11882

Cov.:

AF XY:

0.117

AC XY:

85221

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.349

Gnomad4 AMR exome

AF:

0.0689

Gnomad4 ASJ exome

AF:

0.133

Gnomad4 EAS exome

AF:

0.00997

Gnomad4 SAS exome

AF:

0.0855

Gnomad4 FIN exome

AF:

0.178

Gnomad4 NFE exome

AF:

0.117

Gnomad4 OTH exome

AF:

0.128

GnomAD4 genome

AF:

0.175

AC:

26646

AN:

152052

Hom.:

3218

Cov.:

AF XY:

0.172

AC XY:

12814

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.334

Gnomad4 AMR

AF:

0.109

Gnomad4 ASJ

AF:

0.142

Gnomad4 EAS

AF:

0.00541

Gnomad4 SAS

AF:

0.0730

Gnomad4 FIN

AF:

0.172

Gnomad4 NFE

AF:

0.119

Gnomad4 OTH

AF:

0.140

Alfa

AF:

0.150

Hom.:

1115

Bravo

AF:

0.177

TwinsUK

AF:

0.121

AC:

450

ALSPAC

AF:

0.122

AC:

471

ESP6500AA

AF:

0.338

AC:

1490

ESP6500EA

AF:

0.120

AC:

1031

ExAC

AF:

0.123

AC:

14908

Asia WGS

AF:

0.0610

AC:

213

AN:

3478

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	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.040

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.51

CADD

Benign

4.0

DANN

Benign

0.79

DEOGEN2

Benign

0.049

FATHMM_MKL

Benign

0.017

LIST_S2

Benign

0.24

MetaRNN

Benign

0.0058

PrimateAI

Pathogenic

0.79

Sift4G

Benign

1.0

Vest4

0.071

GERP RS

1.9

Varity_R

0.070

gMVP

0.25

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