ENST00000426701.1:n.694G>A

Variant names:

• chr7-138703034-G-A
• rs6957669
• ENST00000426701.1:n.694G>A

Variant summary

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

The ENST00000426701.1(UQCRFS1P2):​n.694G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.224 in 152,786 control chromosomes in the GnomAD database, including 4,081 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 0.22 (4064 hom., cov: 31)
  • Exomes 𝑓: 0.19 (17 hom.)
• Consequence: UQCRFS1P2 ENST00000426701.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.40
• Publications: 3 publications found

Genes affected

UQCRFS1P2 (HGNC:39172): (ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UQCRFS1P2	ENST00000426701.1	n.694G>A		non_coding_transcript_exon_variant	Exon 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34130 AN: 151874 Hom.: 4058 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0509

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.252

GnomAD4 exome AF: 0.191 AC: 152 AN: 794 Hom.: 17 Cov.: 0 AF XY: 0.202 AC XY: 97 AN XY: 480

African (AFR) AF: 0.286 AC: 20 AN: 70

American (AMR) AF: 0.250 AC: 2 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.0685 AC: 10 AN: 146

South Asian (SAS) AF: 0.250 AC: 8 AN: 32

European-Finnish (FIN) AF: 0.236 AC: 43 AN: 182

Middle Eastern (MID) AF: 0.240 AC: 12 AN: 50

European-Non Finnish (NFE) AF: 0.179 AC: 47 AN: 262

Other (OTH) AF: 0.214 AC: 9 AN: 42

GnomAD4 genome AF: 0.225 AC: 34148 AN: 151992 Hom.: 4064 Cov.: 31 AF XY: 0.223 AC XY: 16552 AN XY: 74316

African (AFR) AF: 0.279 AC: 11570 AN: 41440

American (AMR) AF: 0.202 AC: 3074 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3468

East Asian (EAS) AF: 0.0509 AC: 263 AN: 5172

South Asian (SAS) AF: 0.213 AC: 1024 AN: 4816

European-Finnish (FIN) AF: 0.192 AC: 2028 AN: 10578

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14371 AN: 67960

Other (OTH) AF: 0.250 AC: 527 AN: 2106

Alfa AF: 0.219 Hom.: 11494

Bravo AF: 0.227

Asia WGS AF: 0.146 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.4
DANN	Benign	0.49
PhyloP100		4.4

Splicing

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

Other links and lift over

dbSNP: rs6957669; hg19: chr7-138387779;