3-46310893-T-C

Position:

• chr3-46310893-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000417777.1(UQCRC2P1):​n.1030A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,168 control chromosomes in the GnomAD database, including 41,615 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 0.74 (41615 hom., cov: 33)
  • Exomes 𝑓: 0.93 (1056 hom.)
  • Failed GnomAD Quality Control
• Consequence: UQCRC2P1 ENST00000417777.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

Genes affected

UQCRC2P1 (HGNC:44309): (ubiquinol-cytochrome c reductase core protein 2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCRC2P1	ENST00000417777.1	n.1030A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111856 AN: 152050 Hom.: 41555 Cov.: 33

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.714

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.929 AC: 2278 AN: 2452 Hom.: 1056 Cov.: 0 AF XY: 0.916 AC XY: 1151 AN XY: 1256

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.909

Gnomad4 ASJ exome AF: 0.917

Gnomad4 EAS exome AF: 0.980

Gnomad4 SAS exome AF: 0.917

Gnomad4 FIN exome AF: 0.913

Gnomad4 NFE exome AF: 0.928

Gnomad4 OTH exome AF: 0.959

GnomAD4 genome AF: 0.736 AC: 111968 AN: 152168 Hom.: 41615 Cov.: 33 AF XY: 0.732 AC XY: 54450 AN XY: 74402

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.717

Alfa AF: 0.697 Hom.: 77443

Bravo AF: 0.743

Asia WGS AF: 0.712 AC: 2479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	5.6
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6441961; hg19: chr3-46352384;