dbSNP rs1258470: NDUFB8P3:n.34707718C>T (chr11-34707718-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 variant allele was found at a frequency of 0.511 in 152,118 control chromosomes in the GnomAD database, including 20,642 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 0.51 ( 20642 hom., cov: 32)

Consequence

NDUFB8P3
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84

Publications

3 publications found

Variant links:

Genes affected

NDUFB8P3 (HGNC:33979):

NDUFB8P3 links:

ENSG00000309692 (HGNC:):

ENSG00000309692 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFB8P3		n.34707718C>T		intragenic_variant
LOC102723568	XR_007062652.1 link	n.297-6976C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000309692	ENST00000843048.1 link	n.506+14829C>T	intron_variant	Intron 1 of 2
ENSG00000309692	ENST00000843049.1 link	n.698+5703C>T	intron_variant	Intron 2 of 3
ENSG00000309692	ENST00000843050.1 link	n.290+14829C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.511

AC:

77722

AN:

152000

Hom.:

20617

Cov.:

show subpopulations

Gnomad AFR

AF:

0.570

Gnomad AMI

AF:

0.758

Gnomad AMR

AF:

0.385

Gnomad ASJ

AF:

0.548

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.468

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.540

Gnomad OTH

AF:

0.523

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

GnomAD4 genome

AF:

0.511

AC:

77785

AN:

152118

Hom.:

20642

Cov.:

AF XY:

0.502

AC XY:

37358

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.570

AC:

23664

AN:

41498

American (AMR)

AF:

0.384

AC:

5879

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.548

AC:

1903

AN:

3470

East Asian (EAS)

AF:

0.131

AC:

677

AN:

5166

South Asian (SAS)

AF:

0.428

AC:

2066

AN:

4822

European-Finnish (FIN)

AF:

0.468

AC:

4939

AN:

10556

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.540

AC:

36732

AN:

67986

Other (OTH)

AF:

0.517

AC:

1095

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1917

3834

5750

7667

9584

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<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:

0.518

Hom.:

3577

Bravo

AF:

0.503

Asia WGS

AF:

0.245

AC:

854

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.7

(source)

DANN

Benign

0.71

PhyloP100

-1.8

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