20-35405288-A-G

Variant names:

• chr20-35405288-A-G
• rs1204660
• NM_018244.5:c.24+6652T>C

Variant summary

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

The NM_018244.5(UQCC1):​c.24+6652T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,198 control chromosomes in the GnomAD database, including 61,229 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 0.90 (61229 hom., cov: 32)
• Consequence: UQCC1 NM_018244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 14 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UQCC1	NM_018244.5	MANE Select	c.24+6652T>C		intron	N/A	NP_060714.3
	UQCC1	NM_199487.3		c.24+6652T>C		intron	N/A	NP_955781.2	Q9NVA1-2
	UQCC1	NM_001184977.2		c.24+6652T>C		intron	N/A	NP_001171906.1	Q9NVA1-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UQCC1	ENST00000374385.10	TSL:1 MANE Select	c.24+6652T>C		intron	N/A	ENSP00000363506.5	Q9NVA1-1
	UQCC1	ENST00000457259.5	TSL:1	n.18+6652T>C		intron	N/A	ENSP00000411024.1	H7C3C3
	UQCC1	ENST00000491040.5	TSL:1	n.24+6652T>C		intron	N/A	ENSP00000420584.1	D6RDV2

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136135 AN: 152080 Hom.: 61164 Cov.: 32

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.806

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.895 AC: 136259 AN: 152198 Hom.: 61229 Cov.: 32 AF XY: 0.896 AC XY: 66693 AN XY: 74424

African (AFR) AF: 0.974 AC: 40453 AN: 41526

American (AMR) AF: 0.891 AC: 13620 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2949 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5106 AN: 5182

South Asian (SAS) AF: 0.924 AC: 4462 AN: 4828

European-Finnish (FIN) AF: 0.861 AC: 9119 AN: 10590

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.849 AC: 57732 AN: 67998

Other (OTH) AF: 0.882 AC: 1865 AN: 2114

Alfa AF: 0.864 Hom.: 164492

Bravo AF: 0.901

Asia WGS AF: 0.941 AC: 3271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.5
DANN	Benign	0.80
PhyloP100		-1.8
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: rs1204660; hg19: chr20-33993091;