Genetic Variant ENSG00000309692:n.161C>T (chr11-34680819-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000843053.1(ENSG00000309692):n.161C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,068 control chromosomes in the GnomAD database, including 3,089 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 0.19 ( 3089 hom., cov: 32)

Consequence

ENSG00000309692
ENST00000843053.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.129

Publications

4 publications found

Variant links:

Genes affected

ENSG00000309692 (HGNC:):

ENSG00000309692 links:

NDUFB8P3 (HGNC:33979):

NDUFB8P3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFB8P3		n.34680819C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000309692	ENST00000843053.1 link	n.161C>T	non_coding_transcript_exon_variant	Exon 1 of 5
ENSG00000309708	ENST00000843229.1 link	n.488+4420G>A	intron_variant	Intron 2 of 5
ENSG00000309708	ENST00000843230.1 link	n.532+4420G>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29608

AN:

151950

Hom.:

3085

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.308

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.204

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.195

AC:

29644

AN:

152068

Hom.:

3089

Cov.:

AF XY:

0.196

AC XY:

14543

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.150

AC:

6231

AN:

41468

American (AMR)

AF:

0.308

AC:

4702

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.197

AC:

683

AN:

3468

East Asian (EAS)

AF:

0.128

AC:

660

AN:

5176

South Asian (SAS)

AF:

0.132

AC:

637

AN:

4826

European-Finnish (FIN)

AF:

0.198

AC:

2102

AN:

10592

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

14004

AN:

67970

Other (OTH)

AF:

0.211

AC:

446

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1191

2382

3574

4765

5956

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

320

640

960

1280

1600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.211

Hom.:

641

Bravo

AF:

0.206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.5

(source)

DANN

Benign

0.34

PhyloP100

-0.13

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over