chr20-35319358-T-C

Variant names:

• chr20-35319358-T-C
• rs6060369
• NM_018244.5:c.574-4593A>G

Variant summary

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

The NM_018244.5(UQCC1):​c.574-4593A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,042 control chromosomes in the GnomAD database, including 19,334 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 0.48 (19334 hom., cov: 32)
• Consequence: UQCC1 NM_018244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 87 publications found

Genes affected

UQCC1 (HGNC:15891): (ubiquinol-cytochrome c reductase complex assembly factor 1) This gene encodes a transmembrane protein that is structurally similar to the mouse basic fibroblast growth factor repressed ZIC-binding protein. In mouse this protein may be involved in fibroblast growth factor regulated growth control. In humans, polymorphisms in this gene are associated with variation in human height and osteoarthritis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018244.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UQCC1	NM_018244.5	MANE Select	c.574-4593A>G		intron	N/A	NP_060714.3
	UQCC1	NM_199487.3		c.574-12579A>G		intron	N/A	NP_955781.2
	UQCC1	NM_001184977.2		c.370-4593A>G		intron	N/A	NP_001171906.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UQCC1	ENST00000374385.10	TSL:1 MANE Select	c.574-4593A>G		intron	N/A	ENSP00000363506.5
	UQCC1	ENST00000397556.7	TSL:1	c.355-4593A>G		intron	N/A	ENSP00000380688.4
	UQCC1	ENST00000457259.5	TSL:1	n.*126-4593A>G		intron	N/A	ENSP00000411024.1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72975 AN: 151924 Hom.: 19272 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.456

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.481 AC: 73091 AN: 152042 Hom.: 19334 Cov.: 32 AF XY: 0.482 AC XY: 35827 AN XY: 74306

African (AFR) AF: 0.711 AC: 29459 AN: 41458

American (AMR) AF: 0.358 AC: 5469 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1545 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1434 AN: 5176

South Asian (SAS) AF: 0.555 AC: 2673 AN: 4812

European-Finnish (FIN) AF: 0.452 AC: 4777 AN: 10570

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26260 AN: 67964

Other (OTH) AF: 0.462 AC: 977 AN: 2114

Alfa AF: 0.415 Hom.: 43815

Bravo AF: 0.475

Asia WGS AF: 0.500 AC: 1739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.71
PhyloP100		0.011
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: rs6060369; hg19: chr20-33907161;