chr19-29212182-C-T

Variant summary

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

The NM_006003.3(UQCRFS1):​c.214+723G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,978 control chromosomes in the GnomAD database, including 18,748 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 0.48 ( 18748 hom., cov: 32)

Consequence

UQCRFS1
NM_006003.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.313
Variant links:
Genes affected
UQCRFS1 (HGNC:12587): (ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1) Predicted to enable oxidoreductase activity. Involved in mitochondrial respiratory chain complex III assembly and respiratory electron transport chain. Located in mitochondrion. Part of mitochondrial respiratory chain complex III and mitochondrial respiratory chain complex IV. Implicated in mitochondrial complex III deficiency. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
UQCRFS1NM_006003.3 linkuse as main transcriptc.214+723G>A intron_variant ENST00000304863.6 NP_005994.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UQCRFS1ENST00000304863.6 linkuse as main transcriptc.214+723G>A intron_variant 1 NM_006003.3 ENSP00000306397 P1

Frequencies

GnomAD3 genomes
AF:
0.479
AC:
72769
AN:
151860
Hom.:
18720
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.677
Gnomad AMI
AF:
0.286
Gnomad AMR
AF:
0.467
Gnomad ASJ
AF:
0.454
Gnomad EAS
AF:
0.519
Gnomad SAS
AF:
0.467
Gnomad FIN
AF:
0.350
Gnomad MID
AF:
0.506
Gnomad NFE
AF:
0.383
Gnomad OTH
AF:
0.503
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.479
AC:
72857
AN:
151978
Hom.:
18748
Cov.:
32
AF XY:
0.478
AC XY:
35495
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.677
Gnomad4 AMR
AF:
0.467
Gnomad4 ASJ
AF:
0.454
Gnomad4 EAS
AF:
0.519
Gnomad4 SAS
AF:
0.468
Gnomad4 FIN
AF:
0.350
Gnomad4 NFE
AF:
0.383
Gnomad4 OTH
AF:
0.500
Alfa
AF:
0.438
Hom.:
3166
Bravo
AF:
0.493
Asia WGS
AF:
0.461
AC:
1603
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
2.3
DANN
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs10420904; hg19: chr19-29703089; API