chr16-21957068-CA-C

Position:

• chr16-21957068-CA-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_003366.4(UQCRC2):​c.34-151del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0099 (4 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: UQCRC2 NM_003366.4 intron
• Clinical Significance: Likely 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 Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 16-21957068-CA-C is Benign according to our data. Variant chr16-21957068-CA-C is described in ClinVar as [Likely_benign]. Clinvar id is 1198507.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UQCRC2	NM_003366.4	c.34-151del		intron_variant		ENST00000268379.9	NP_003357.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UQCRC2	ENST00000268379.9	c.34-151del		intron_variant		1	NM_003366.4	ENSP00000268379	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1010 AN: 102948 Hom.: 4 Cov.: 31 FAILED QC

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00617

Gnomad ASJ AF: 0.00274

Gnomad EAS AF: 0.00164

Gnomad SAS AF: 0.0208

Gnomad FIN AF: 0.0217

Gnomad MID AF: 0.0211

Gnomad NFE AF: 0.00324

Gnomad OTH AF: 0.00706

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00986 AC: 1015 AN: 102942 Hom.: 4 Cov.: 31 AF XY: 0.0107 AC XY: 526 AN XY: 49190

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.00616

Gnomad4 ASJ AF: 0.00274

Gnomad4 EAS AF: 0.00165

Gnomad4 SAS AF: 0.0209

Gnomad4 FIN AF: 0.0217

Gnomad4 NFE AF: 0.00324

Gnomad4 OTH AF: 0.00705

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely 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;