NM_018244.5:c.130-3245G>T

Variant names:

• chr20-35387378-C-A
• rs6088813
• NM_018244.5:c.130-3245G>T

Variant summary

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

The NM_018244.5(UQCC1):​c.130-3245G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,984 control chromosomes in the GnomAD database, including 23,434 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 0.54 (23434 hom., cov: 31)
• Consequence: UQCC1 NM_018244.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 60 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UQCC1	NM_018244.5	c.130-3245G>T		intron_variant	Intron 2 of 9	ENST00000374385.10	NP_060714.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UQCC1	ENST00000374385.10	c.130-3245G>T		intron_variant	Intron 2 of 9	1	NM_018244.5	ENSP00000363506.5

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82493 AN: 151866 Hom.: 23428 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.543 AC: 82504 AN: 151984 Hom.: 23434 Cov.: 31 AF XY: 0.541 AC XY: 40223 AN XY: 74284

African (AFR) AF: 0.365 AC: 15139 AN: 41444

American (AMR) AF: 0.649 AC: 9904 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1927 AN: 3468

East Asian (EAS) AF: 0.716 AC: 3713 AN: 5188

South Asian (SAS) AF: 0.443 AC: 2132 AN: 4812

European-Finnish (FIN) AF: 0.572 AC: 6028 AN: 10532

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41777 AN: 67952

Other (OTH) AF: 0.557 AC: 1177 AN: 2112

Alfa AF: 0.593 Hom.: 99108

Bravo AF: 0.549

Asia WGS AF: 0.483 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.81
DANN	Benign	0.52
PhyloP100		-0.57
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: rs6088813; hg19: chr20-33975181;