Variant 7-138703034-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.40

Variant links:

Genes affected

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

UQCRFS1P2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UQCRFS1P2	ENST00000426701.1 linkuse as main transcript	n.694G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes

AF:

0.225

AC:

34130

AN:

151874

Hom.:

4058

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.202

AC XY:

AN XY:

480

show subpopulations

Gnomad4 AFR exome

AF:

0.286

Gnomad4 AMR exome

AF:

0.250

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.0685

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.236

Gnomad4 NFE exome

AF:

0.179

Gnomad4 OTH exome

AF:

0.214

GnomAD4 genome

AF:

0.225

AC:

34148

AN:

151992

Hom.:

4064

Cov.:

AF XY:

0.223

AC XY:

16552

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.279

Gnomad4 AMR

AF:

0.202

Gnomad4 ASJ

AF:

0.306

Gnomad4 EAS

AF:

0.0509

Gnomad4 SAS

AF:

0.213

Gnomad4 FIN

AF:

0.192

Gnomad4 NFE

AF:

0.211

Gnomad4 OTH

AF:

0.250

Alfa

AF:

0.224

Hom.:

4866

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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over