chr6-33697857-CAG-C

Position:

• chr6-33697857-CAG-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_032340.4(UQCC2):​c.284-109_284-108del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0195 in 847,292 control chromosomes in the GnomAD database, including 225 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.014 (34 hom., cov: 33)
  • Exomes 𝑓: 0.021 (191 hom.)
• Consequence: UQCC2 NM_032340.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.24

Genes affected

UQCC2 (HGNC:21237): (ubiquinol-cytochrome c reductase complex assembly factor 2) This gene encodes a nucleoid protein localized to the mitochondria inner membrane. The encoded protein affects regulation of insulin secretion, mitochondrial ATP production, and myogenesis through modulation of mitochondrial respiratory chain activity. [provided by RefSeq, Oct 2012]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-33697857-CAG-C is Benign according to our data. Variant chr6-33697857-CAG-C is described in ClinVar as [Likely_benign]. Clinvar id is 1210844.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0145 (2206/152370) while in subpopulation NFE AF= 0.0252 (1716/68042). AF 95% confidence interval is 0.0242. There are 34 homozygotes in gnomad4. There are 973 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 34 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UQCC2	NM_032340.4	c.284-109_284-108del		intron_variant		ENST00000607484.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCC2	ENST00000607484.6	c.284-109_284-108del		intron_variant		1	NM_032340.4	P1
UQCC2	ENST00000374214.3	c.209-109_209-108del		intron_variant		5
UQCC2	ENST00000374231.8	c.282-109_282-108del		intron_variant		3
UQCC2	ENST00000606961.1	n.799_800del		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0145 AC: 2206 AN: 152252 Hom.: 34 Cov.: 33

Gnomad AFR AF: 0.00485

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.00582

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00612

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0252

Gnomad OTH AF: 0.0110

GnomAD4 exome AF: 0.0207 AC: 14353 AN: 694922 Hom.: 191 AF XY: 0.0197 AC XY: 7111 AN XY: 361566

Gnomad4 AFR exome AF: 0.00433

Gnomad4 AMR exome AF: 0.00669

Gnomad4 ASJ exome AF: 0.0209

Gnomad4 EAS exome AF: 0.0000576

Gnomad4 SAS exome AF: 0.00111

Gnomad4 FIN exome AF: 0.00923

Gnomad4 NFE exome AF: 0.0267

Gnomad4 OTH exome AF: 0.0198

GnomAD4 genome AF: 0.0145 AC: 2206 AN: 152370 Hom.: 34 Cov.: 33 AF XY: 0.0131 AC XY: 973 AN XY: 74504

Gnomad4 AFR AF: 0.00483

Gnomad4 AMR AF: 0.00581

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00612

Gnomad4 NFE AF: 0.0252

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.0197 Hom.: 9

Bravo AF: 0.0153

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

Jun 29, 2018

- -

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: rs550441724; hg19: chr6-33665634;