6-33697932-G-A

Position:

• chr6-33697932-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_032340.4(UQCC2):​c.284-182C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 596,848 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0032 (2 hom., cov: 33)
  • Exomes 𝑓: 0.00048 (1 hom.)
• Consequence: UQCC2 NM_032340.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.03

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.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 6-33697932-G-A is Benign according to our data. Variant chr6-33697932-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1193007.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UQCC2	NM_032340.4	c.284-182C>T		intron_variant		ENST00000607484.6	NP_115716.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UQCC2	ENST00000607484.6	c.284-182C>T		intron_variant		1	NM_032340.4	ENSP00000476140	P1
UQCC2	ENST00000374214.3	c.209-182C>T		intron_variant		5		ENSP00000363331
UQCC2	ENST00000374231.8	c.282-182C>T		intron_variant		3		ENSP00000363348
UQCC2	ENST00000606961.1	n.726C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.00323 AC: 491 AN: 152246 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000981

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00334

GnomAD4 exome AF: 0.000481 AC: 214 AN: 444484 Hom.: 1 Cov.: 3 AF XY: 0.000381 AC XY: 90 AN XY: 235990

Gnomad4 AFR exome AF: 0.0104

Gnomad4 AMR exome AF: 0.00116

Gnomad4 ASJ exome AF: 0.000822

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000440

Gnomad4 FIN exome AF: 0.0000352

Gnomad4 NFE exome AF: 0.000101

Gnomad4 OTH exome AF: 0.000856

GnomAD4 genome AF: 0.00322 AC: 490 AN: 152364 Hom.: 2 Cov.: 33 AF XY: 0.00306 AC XY: 228 AN XY: 74510

Gnomad4 AFR AF: 0.0111

Gnomad4 AMR AF: 0.000980

Gnomad4 ASJ AF: 0.000577

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00298 Hom.: 0

Bravo AF: 0.00378

Asia WGS AF: 0.000289 AC: 1 AN: 3478

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 25, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.78

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: rs190812550; hg19: chr6-33665709;