chr16-21957068-C-CA

Position:

• chr16-21957068-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003366.4(UQCRC2):​c.34-151dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0654 in 102,956 control chromosomes in the GnomAD database, including 179 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.065 (179 hom., cov: 31)
• Consequence: UQCRC2 NM_003366.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0570

Genes affected

UQCRC2 (HGNC:12586): (ubiquinol-cytochrome c reductase core protein 2) The protein encoded by this gene is located in the mitochondrion, where it is part of the ubiquinol-cytochrome c reductase complex (also known as complex III). This complex constitutes a part of the mitochondrial respiratory chain. Defects in this gene are a cause of mitochondrial complex III deficiency nuclear type 5. [provided by RefSeq, Jul 2015]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 16-21957068-C-CA is Benign according to our data. Variant chr16-21957068-C-CA is described in ClinVar as [Benign]. Clinvar id is 1236238.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UQCRC2	NM_003366.4	c.34-151dup		intron_variant		ENST00000268379.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCRC2	ENST00000268379.9	c.34-151dup		intron_variant		1	NM_003366.4	P1

Frequencies

GnomAD3 genomes AF: 0.0654 AC: 6734 AN: 102958 Hom.: 179 Cov.: 31

Gnomad AFR AF: 0.0389

Gnomad AMI AF: 0.0765

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.0497

Gnomad EAS AF: 0.0597

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.0474

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.0705

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

GnomAD4 genome AF: 0.0654 AC: 6729 AN: 102956 Hom.: 179 Cov.: 31 AF XY: 0.0641 AC XY: 3151 AN XY: 49184

Gnomad4 AFR AF: 0.0389

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.0497

Gnomad4 EAS AF: 0.0594

Gnomad4 SAS AF: 0.0171

Gnomad4 FIN AF: 0.0829

Gnomad4 NFE AF: 0.0819

Gnomad4 OTH AF: 0.0696

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 24, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs35025046; hg19: chr16-21968389;