chr3-46310893-T-C

Variant names:

• chr3-46310893-T-C
• rs6441961
• ENST00000417777.1:n.1030A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 53 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417777.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UQCRC2P1	ENST00000417777.1	TSL:6	n.1030A>G		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 1.00 AC: 20 AN: 20

American (AMR) AF: 0.909 AC: 20 AN: 22

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 33 AN: 36

East Asian (EAS) AF: 0.980 AC: 49 AN: 50

South Asian (SAS) AF: 0.917 AC: 253 AN: 276

European-Finnish (FIN) AF: 0.913 AC: 126 AN: 138

Middle Eastern (MID) AF: 0.750 AC: 3 AN: 4

European-Non Finnish (NFE) AF: 0.928 AC: 1609 AN: 1734

Other (OTH) AF: 0.959 AC: 165 AN: 172

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

African (AFR) AF: 0.850 AC: 35292 AN: 41510

American (AMR) AF: 0.675 AC: 10320 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2546 AN: 3466

East Asian (EAS) AF: 0.697 AC: 3611 AN: 5184

South Asian (SAS) AF: 0.658 AC: 3171 AN: 4822

European-Finnish (FIN) AF: 0.711 AC: 7529 AN: 10590

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.694 AC: 47198 AN: 67990

Other (OTH) AF: 0.717 AC: 1512 AN: 2110

Alfa AF: 0.707 Hom.: 122456

Bravo AF: 0.743

Asia WGS AF: 0.712 AC: 2479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	5.6
DANN	Benign	0.74
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6441961; hg19: chr3-46352384;