6-33700261-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_032340.4(UQCC2):​c.283+183C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0519 in 152,046 control chromosomes in the GnomAD database, including 343 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.052 ( 343 hom., cov: 33)

Consequence

UQCC2
NM_032340.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.360
Variant links:
Genes affected
UQCC2 (HGNC:21237): (ubiquinol-cytochrome c reductase complex assembly factor 2) This gene encodes a nucleoid protein localized to the mitochondria inner membrane. The encoded protein affects regulation of insulin secretion, mitochondrial ATP production, and myogenesis through modulation of mitochondrial respiratory chain activity. [provided by RefSeq, Oct 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 6-33700261-G-A is Benign according to our data. Variant chr6-33700261-G-A is described in ClinVar as [Benign]. Clinvar id is 684316.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
UQCC2NM_032340.4 linkuse as main transcriptc.283+183C>T intron_variant ENST00000607484.6 NP_115716.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UQCC2ENST00000607484.6 linkuse as main transcriptc.283+183C>T intron_variant 1 NM_032340.4 ENSP00000476140 P1
UQCC2ENST00000374214.3 linkuse as main transcriptc.208+183C>T intron_variant 5 ENSP00000363331
UQCC2ENST00000374231.8 linkuse as main transcriptc.281+183C>T intron_variant 3 ENSP00000363348

Frequencies

GnomAD3 genomes
AF:
0.0517
AC:
7861
AN:
151928
Hom.:
338
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.00329
Gnomad AMR
AF:
0.0321
Gnomad ASJ
AF:
0.0144
Gnomad EAS
AF:
0.0385
Gnomad SAS
AF:
0.0468
Gnomad FIN
AF:
0.0196
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0216
Gnomad OTH
AF:
0.0531
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0519
AC:
7897
AN:
152046
Hom.:
343
Cov.:
33
AF XY:
0.0520
AC XY:
3861
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.124
Gnomad4 AMR
AF:
0.0320
Gnomad4 ASJ
AF:
0.0144
Gnomad4 EAS
AF:
0.0386
Gnomad4 SAS
AF:
0.0473
Gnomad4 FIN
AF:
0.0196
Gnomad4 NFE
AF:
0.0216
Gnomad4 OTH
AF:
0.0559
Alfa
AF:
0.0354
Hom.:
40
Bravo
AF:
0.0553
Asia WGS
AF:
0.0620
AC:
216
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 14, 2018This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.65
CADD
Benign
12
DANN
Benign
0.71

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: rs74330951; hg19: chr6-33668038; API