rs11588062

chr1-46314092-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006004.4(UQCRH):c.244-2460C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,968 control chromosomes in the GnomAD database, including 6,315 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (6315 hom., cov: 32)
• Consequence: UQCRH NM_006004.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

Genes affected

UQCRH (HGNC:12590): (ubiquinol-cytochrome c reductase hinge protein) Predicted to enable ubiquinol-cytochrome-c reductase activity. Predicted to be involved in mitochondrial electron transport, ubiquinol to cytochrome c. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UQCRH	NM_006004.4	c.244-2460C>T		intron_variant		ENST00000311672.10
UQCRH	NM_001297565.2	c.226-2460C>T		intron_variant
UQCRH	NM_001297566.2	c.217-2460C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCRH	ENST00000311672.10	c.244-2460C>T		intron_variant		1	NM_006004.4	P1
UQCRH	ENST00000496387.5	c.*83-2460C>T		intron_variant, NMD_transcript_variant		1
UQCRH	ENST00000489056.5	c.*83-2460C>T		intron_variant, NMD_transcript_variant		2
UQCRH	ENST00000460947.1	n.397-2460C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39560 AN: 151850 Hom.: 6322 Cov.: 32

Gnomad AFR AF: 0.0814

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.293

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.260 AC: 39549 AN: 151968 Hom.: 6315 Cov.: 32 AF XY: 0.260 AC XY: 19319 AN XY: 74244

Gnomad4 AFR AF: 0.0812

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.289

Alfa AF: 0.289 Hom.: 1562

Bravo AF: 0.263

Asia WGS AF: 0.348 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.85
Dann	Benign	0.80

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

Other links and lift over

dbSNP: rs11588062; hg19: chr1-46779764; COSMIC: COSV61176074; COSMIC: COSV61176074;