chr20-35321981-C-T

Variant names:

• chr20-35321981-C-T
• rs6088792
• NM_018244.5:c.574-7216G>A

Variant summary

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

The NM_018244.5(UQCC1):​c.574-7216G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,106 control chromosomes in the GnomAD database, including 5,529 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 0.26 (5529 hom., cov: 32)
• Consequence: UQCC1 NM_018244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 44 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UQCC1	NM_018244.5	c.574-7216G>A		intron_variant	Intron 7 of 9	ENST00000374385.10	NP_060714.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UQCC1	ENST00000374385.10	c.574-7216G>A		intron_variant	Intron 7 of 9	1	NM_018244.5	ENSP00000363506.5

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39371 AN: 151988 Hom.: 5529 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.259 AC: 39371 AN: 152106 Hom.: 5529 Cov.: 32 AF XY: 0.261 AC XY: 19393 AN XY: 74352

African (AFR) AF: 0.178 AC: 7406 AN: 41510

American (AMR) AF: 0.242 AC: 3700 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1129 AN: 3464

East Asian (EAS) AF: 0.106 AC: 550 AN: 5184

South Asian (SAS) AF: 0.247 AC: 1192 AN: 4820

European-Finnish (FIN) AF: 0.373 AC: 3937 AN: 10544

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20475 AN: 67986

Other (OTH) AF: 0.266 AC: 563 AN: 2114

Alfa AF: 0.281 Hom.: 22482

Bravo AF: 0.244

Asia WGS AF: 0.202 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
DANN	Benign	0.38
PhyloP100		0.0060
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: rs6088792; hg19: chr20-33909784;