16-21957068-C-A

Position:

• chr16-21957068-C-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The ENST00000268379.9(UQCRC2):​c.34-167C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0039 (0 hom., cov: 27)
  • Failed GnomAD Quality Control
• Consequence: UQCRC2 ENST00000268379.9 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.05

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 -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 16-21957068-C-A is Benign according to our data. Variant chr16-21957068-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1217044.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.34-167C>A		intron_variant		ENST00000268379.9	NP_003357.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UQCRC2	ENST00000268379.9	c.34-167C>A		intron_variant		1	NM_003366.4	ENSP00000268379	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 403 AN: 102526 Hom.: 0 Cov.: 27 FAILED QC

Gnomad AFR AF: 0.00368

Gnomad AMI AF: 0.00814

Gnomad AMR AF: 0.00383

Gnomad ASJ AF: 0.00118

Gnomad EAS AF: 0.000825

Gnomad SAS AF: 0.00235

Gnomad FIN AF: 0.0176

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00287

Gnomad OTH AF: 0.00553

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: 0.00393 AC: 403 AN: 102526 Hom.: 0 Cov.: 27 AF XY: 0.00420 AC XY: 206 AN XY: 48996

Gnomad4 AFR AF: 0.00367

Gnomad4 AMR AF: 0.00383

Gnomad4 ASJ AF: 0.00118

Gnomad4 EAS AF: 0.000829

Gnomad4 SAS AF: 0.00236

Gnomad4 FIN AF: 0.0176

Gnomad4 NFE AF: 0.00287

Gnomad4 OTH AF: 0.00552

Alfa AF: 0.00554 Hom.: 0

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

Aug 21, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.29
DANN	Benign	0.76

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: rs74791900; hg19: chr16-21968389;