Variant rs2302175 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_004548.3(NDUFB10):c.72C>T(p.Ile24=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0343 in 1,613,348 control chromosomes in the GnomAD database, including 3,590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.070 ( 789 hom., cov: 33)

Exomes 𝑓: 0.031 ( 2801 hom. )

Consequence

NDUFB10
NM_004548.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.261

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 16-1959696-C-T is Benign according to our data. Variant chr16-1959696-C-T is described in ClinVar as [Benign]. Clinvar id is 2014724.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.261 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDUFB10	NM_004548.3 linkuse as main transcript	c.72C>T	p.Ile24=	synonymous_variant	1/4	ENST00000268668.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDUFB10	ENST00000268668.11 linkuse as main transcript	c.72C>T	p.Ile24=	synonymous_variant	1/4	1	NM_004548.3	P1	O96000-1

Frequencies

GnomAD3 genomes

AF:

0.0705

AC:

10725

AN:

152078

Hom.:

791

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0511

Gnomad ASJ

AF:

0.0308

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.0458

Gnomad FIN

AF:

0.0508

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0170

Gnomad OTH

AF:

0.0675

GnomAD3 exomes

AF:

0.0575

AC:

14384

AN:

250350

Hom.:

1214

AF XY:

0.0535

AC XY:

7251

AN XY:

135610

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.0389

Gnomad ASJ exome

AF:

0.0352

Gnomad EAS exome

AF:

0.305

Gnomad SAS exome

AF:

0.0414

Gnomad FIN exome

AF:

0.0517

Gnomad NFE exome

AF:

0.0171

Gnomad OTH exome

AF:

0.0386

GnomAD4 exome

AF:

0.0305

AC:

44570

AN:

1461152

Hom.:

2801

Cov.:

AF XY:

0.0304

AC XY:

22095

AN XY:

726892

show subpopulations

Gnomad4 AFR exome

AF:

0.156

Gnomad4 AMR exome

AF:

0.0407

Gnomad4 ASJ exome

AF:

0.0336

Gnomad4 EAS exome

AF:

0.305

Gnomad4 SAS exome

AF:

0.0400

Gnomad4 FIN exome

AF:

0.0481

Gnomad4 NFE exome

AF:

0.0141

Gnomad4 OTH exome

AF:

0.0439

GnomAD4 genome

AF:

0.0705

AC:

10725

AN:

152196

Hom.:

789

Cov.:

AF XY:

0.0728

AC XY:

5417

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.149

Gnomad4 AMR

AF:

0.0510

Gnomad4 ASJ

AF:

0.0308

Gnomad4 EAS

AF:

0.306

Gnomad4 SAS

AF:

0.0456

Gnomad4 FIN

AF:

0.0508

Gnomad4 NFE

AF:

0.0170

Gnomad4 OTH

AF:

0.0672

Alfa

AF:

0.0301

Hom.:

222

Bravo

AF:

0.0770

Asia WGS

AF:

0.131

AC:

455

AN:

3478

EpiCase

AF:

0.0209

EpiControl

AF:

0.0205

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

Invitae

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

7.1

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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.

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