chr6-33697541-G-A

Position:

• chr6-33697541-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_032340.4(UQCC2):​c.*112C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00504 in 763,856 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.016 (51 hom., cov: 33)
  • Exomes 𝑓: 0.0024 (32 hom.)
• Consequence: UQCC2 NM_032340.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.487

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 6-33697541-G-A is Benign according to our data. Variant chr6-33697541-G-A is described in ClinVar as [Benign]. Clinvar id is 1250225.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UQCC2	NM_032340.4	c.*112C>T		3_prime_UTR_variant	4/4	ENST00000607484.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCC2	ENST00000607484.6	c.*112C>T		3_prime_UTR_variant	4/4	1	NM_032340.4	P1
UQCC2	ENST00000374231.8	c.*30+82C>T		intron_variant		3
UQCC2	ENST00000606961.1	n.1117C>T		non_coding_transcript_exon_variant	1/1
UQCC2	ENST00000374214.3			downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.0156 AC: 2381 AN: 152206 Hom.: 50 Cov.: 33

Gnomad AFR AF: 0.0525

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00752

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000808

Gnomad OTH AF: 0.0139

GnomAD4 exome AF: 0.00239 AC: 1460 AN: 611532 Hom.: 32 Cov.: 8 AF XY: 0.00207 AC XY: 660 AN XY: 319280

Gnomad4 AFR exome AF: 0.0537

Gnomad4 AMR exome AF: 0.00591

Gnomad4 ASJ exome AF: 0.000882

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000245

Gnomad4 FIN exome AF: 0.000250

Gnomad4 NFE exome AF: 0.000718

Gnomad4 OTH exome AF: 0.00478

GnomAD4 genome AF: 0.0157 AC: 2393 AN: 152324 Hom.: 51 Cov.: 33 AF XY: 0.0156 AC XY: 1161 AN XY: 74494

Gnomad4 AFR AF: 0.0526

Gnomad4 AMR AF: 0.00751

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000809

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.0158 Hom.: 7

Bravo AF: 0.0183

Asia WGS AF: 0.00231 AC: 8 AN: 3478

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

Jun 28, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.56

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: rs116538588; hg19: chr6-33665318;