rs6957669

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

2

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)

Genome browser will be placed here

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
UQCRFS1P2ENST00000426701.1 linkuse as main transcriptn.694G>A non_coding_transcript_exon_variant 2/2

Frequencies

GnomAD3 genomes
AF:
0.225
AC:
34130
AN:
151874
Hom.:
4058
Cov.:
31
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.:
17
Cov.:
0
AF XY:
0.202
AC XY:
97
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.:
31
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.

Other links and lift over

dbSNP: rs6957669; hg19: chr7-138387779; API