chr20-35319358-T-C

Position:

• chr20-35319358-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

UQCC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UQCC1	NM_018244.5	c.574-4593A>G		intron_variant		ENST00000374385.10	NP_060714.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UQCC1	ENST00000374385.10	c.574-4593A>G		intron_variant		1	NM_018244.5	ENSP00000363506.5

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

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.462

Alfa AF: 0.401 Hom.: 15296

Bravo AF: 0.475

Asia WGS AF: 0.500 AC: 1739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.71

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: rs6060369; hg19: chr20-33907161;