NR_183272.1:n.131A>G

Variant names:

• chr8-96235770-A-G
• rs73698551
• ENST00000727543.1:n.125A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_183272.1(UQCRB-AS1):​n.131A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000202 in 494,496 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000020 (0 hom.)
• Consequence: UQCRB-AS1 NR_183272.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 0 publications found

Genes affected

UQCRB-AS1 (HGNC:55521): (UQCRB antisense RNA 1)

UQCRB (HGNC:12582): (ubiquinol-cytochrome c reductase binding protein) This gene encodes a subunit of the ubiquinol-cytochrome c oxidoreductase complex, which consists of one mitochondrial-encoded and 10 nuclear-encoded subunits. The protein encoded by this gene binds ubiquinone and participates in the transfer of electrons when ubiquinone is bound. This protein plays an important role in hypoxia-induced angiogenesis through mitochondrial reactive oxygen species-mediated signaling. Mutations in this gene are associated with mitochondrial complex III deficiency. Alternatively spliced transcript variants have been found for this gene. Related pseudogenes have been identified on chromosomes 1, 5 and X. [provided by RefSeq, Dec 2011]

UQCRB Gene-Disease associations (from GenCC):

• mitochondrial complex III deficiency nuclear type 3

  Inheritance: AR, Unknown Classification: STRONG, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• mitochondrial complex III deficiency

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183272.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UQCRB-AS1	NR_183272.1		n.131A>G		non_coding_transcript_exon	Exon 1 of 3
	UQCRB-AS1	NR_183273.1		n.55+76A>G		intron	N/A
	UQCRB-AS1	NR_183274.1		n.269+209A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UQCRB-AS1	ENST00000727543.1		n.125A>G		non_coding_transcript_exon	Exon 1 of 2
	UQCRB-AS1	ENST00000727544.1		n.133A>G		non_coding_transcript_exon	Exon 1 of 3
	UQCRB-AS1	ENST00000520575.2	TSL:2	n.271+209A>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000202 AC: 1 AN: 494496 Hom.: 0 AF XY: 0.00000377 AC XY: 1 AN XY: 265384

African (AFR) AF: 0.00 AC: 0 AN: 14138

American (AMR) AF: 0.00 AC: 0 AN: 28240

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16462

East Asian (EAS) AF: 0.00 AC: 0 AN: 30832

South Asian (SAS) AF: 0.00 AC: 0 AN: 55022

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31266

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2152

European-Non Finnish (NFE) AF: 0.00000346 AC: 1 AN: 288632

Other (OTH) AF: 0.00 AC: 0 AN: 27752

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.0
DANN	Benign	0.71
PhyloP100		-0.15
PromoterAI		-0.024	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs73698551; hg19: chr8-97247998;