chr3-52541815-G-A

Variant names:

• chr3-52541815-G-A
• rs1133415
• NM_001124767.2:c.*1330G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001124767.2(UQCC5):​c.*1330G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,992 control chromosomes in the GnomAD database, including 16,012 homozygotes. 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: 𝑓 0.45 (16012 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: UQCC5 NM_001124767.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 26 publications found

Genes affected

UQCC5 (HGNC:37257): (ubiquinol-cytochrome c reductase complex assembly factor 5) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UQCC5	NM_001124767.2	c.*1330G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000477703.6	NP_001118239.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UQCC5	ENST00000477703.6	c.*1330G>A		3_prime_UTR_variant	Exon 2 of 2	1	NM_001124767.2	ENSP00000417806.1
UQCC5	ENST00000476842.1	c.151+4909G>A		intron_variant	Intron 1 of 1	4		ENSP00000418000.1

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68960 AN: 151874 Hom.: 15998 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.454

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.454 AC: 69023 AN: 151992 Hom.: 16012 Cov.: 32 AF XY: 0.455 AC XY: 33804 AN XY: 74254

African (AFR) AF: 0.393 AC: 16273 AN: 41436

American (AMR) AF: 0.535 AC: 8176 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1718 AN: 3466

East Asian (EAS) AF: 0.430 AC: 2221 AN: 5168

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4820

European-Finnish (FIN) AF: 0.481 AC: 5069 AN: 10544

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32561 AN: 67970

Other (OTH) AF: 0.460 AC: 967 AN: 2104

Alfa AF: 0.458 Hom.: 13772

Bravo AF: 0.458

Asia WGS AF: 0.388 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.74
DANN	Benign	0.59
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1133415; hg19: chr3-52575831;