Variant chr16-1959761-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_004548.3(NDUFB10):c.130+7A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0292 in 1,612,626 control chromosomes in the GnomAD database, including 870 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.038 ( 171 hom., cov: 33)

Exomes 𝑓: 0.028 ( 699 hom. )

Consequence

NDUFB10
NM_004548.3 splice_region, intron

Scores

Splicing: ADA: 0.0003757

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.352

Variant links:

Genes affected

NDUFB10 (HGNC:7696): (NADH:ubiquinone oxidoreductase subunit B10) Involved in mitochondrial respiratory chain complex I assembly. Located in mitochondrial inner membrane. Part of mitochondrial respiratory chain complex I. Implicated in nuclear type mitochondrial complex I deficiency 35. [provided by Alliance of Genome Resources, Apr 2022]

NDUFB10 links:

NDUFB10 (HGNC:):

NDUFB10 links:

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 16-1959761-A-G is Benign according to our data. Variant chr16-1959761-A-G is described in ClinVar as [Benign]. Clinvar id is 2123710.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NDUFB10	NM_004548.3 linkuse as main transcript	c.130+7A>G		splice_region_variant, intron_variant		ENST00000268668.11	NP_004539.1	O96000-1A8K761

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDUFB10	ENST00000268668.11 linkuse as main transcript	c.130+7A>G		splice_region_variant, intron_variant		1	NM_004548.3	ENSP00000268668.6		O96000-1

Frequencies

GnomAD3 genomes

AF:

0.0380

AC:

5780

AN:

151990

Hom.:

169

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0774

Gnomad AMI

AF:

0.0351

Gnomad AMR

AF:

0.0182

Gnomad ASJ

AF:

0.0115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0369

Gnomad FIN

AF:

0.0149

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0269

Gnomad OTH

AF:

0.0263

GnomAD3 exomes

AF:

0.0252

AC:

6269

AN:

248364

Hom.:

131

AF XY:

0.0252

AC XY:

3392

AN XY:

134704

show subpopulations

Gnomad AFR exome

AF:

0.0794

Gnomad AMR exome

AF:

0.00898

Gnomad ASJ exome

AF:

0.00991

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0322

Gnomad FIN exome

AF:

0.0138

Gnomad NFE exome

AF:

0.0284

Gnomad OTH exome

AF:

0.0223

GnomAD4 exome

AF:

0.0282

AC:

41256

AN:

1460518

Hom.:

699

Cov.:

AF XY:

0.0279

AC XY:

20304

AN XY:

726568

show subpopulations

Gnomad4 AFR exome

AF:

0.0779

Gnomad4 AMR exome

AF:

0.0103

Gnomad4 ASJ exome

AF:

0.0111

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0312

Gnomad4 FIN exome

AF:

0.0143

Gnomad4 NFE exome

AF:

0.0293

Gnomad4 OTH exome

AF:

0.0289

GnomAD4 genome

AF:

0.0381

AC:

5790

AN:

152108

Hom.:

171

Cov.:

AF XY:

0.0369

AC XY:

2741

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.0774

Gnomad4 AMR

AF:

0.0182

Gnomad4 ASJ

AF:

0.0115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0372

Gnomad4 FIN

AF:

0.0149

Gnomad4 NFE

AF:

0.0269

Gnomad4 OTH

AF:

0.0260

Alfa

AF:

0.0312

Hom.:

Bravo

AF:

0.0391

Asia WGS

AF:

0.0150

AC:

AN:

3478

EpiCase

AF:

0.0232

EpiControl

AF:

0.0244

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 submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.7

DANN

Benign

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00038

dbscSNV1_RF

Benign

0.0020

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over