chr6-33697848-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_032340.4(UQCC2):​c.284-98G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00145 in 938,254 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0057 ( 14 hom., cov: 33)
Exomes 𝑓: 0.00063 ( 4 hom. )

Consequence

UQCC2
NM_032340.4 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.31
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 6-33697848-C-T is Benign according to our data. Variant chr6-33697848-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1194865.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0057 (868/152298) while in subpopulation AFR AF= 0.0196 (814/41592). AF 95% confidence interval is 0.0185. There are 14 homozygotes in gnomad4. There are 433 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 14 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
UQCC2NM_032340.4 linkuse as main transcriptc.284-98G>A 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.284-98G>A intron_variant 1 NM_032340.4 ENSP00000476140 P1
UQCC2ENST00000374214.3 linkuse as main transcriptc.209-98G>A intron_variant 5 ENSP00000363331
UQCC2ENST00000374231.8 linkuse as main transcriptc.282-98G>A intron_variant 3 ENSP00000363348
UQCC2ENST00000606961.1 linkuse as main transcriptn.810G>A non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.00572
AC:
870
AN:
152180
Hom.:
14
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0197
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00275
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000883
Gnomad OTH
AF:
0.00287
GnomAD4 exome
AF:
0.000629
AC:
494
AN:
785956
Hom.:
4
Cov.:
10
AF XY:
0.000552
AC XY:
225
AN XY:
407242
show subpopulations
Gnomad4 AFR exome
AF:
0.0182
Gnomad4 AMR exome
AF:
0.00212
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000856
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000274
Gnomad4 OTH exome
AF:
0.00156
GnomAD4 genome
AF:
0.00570
AC:
868
AN:
152298
Hom.:
14
Cov.:
33
AF XY:
0.00581
AC XY:
433
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.0196
Gnomad4 AMR
AF:
0.00275
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000883
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.00638
Hom.:
2
Bravo
AF:
0.00669
Asia WGS
AF:
0.000866
AC:
3
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxJun 23, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
0.16
DANN
Benign
0.72

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: rs112204790; hg19: chr6-33665625; API