Variant chr2-239921636-TGCATTTTACAAACCTCTTGCTACTACAGAGCACTGATTGGC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000419408.5(NDUFA10):c.295-26363_295-26323del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0611 in 152,204 control chromosomes in the GnomAD database, including 362 homozygotes. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.061 ( 362 hom., cov: 31)

Consequence

NDUFA10
ENST00000419408.5 intron

Scores

Not classified

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 0.252

Variant links:

Genes affected

NDUFA10 (HGNC:7684): (NADH:ubiquinone oxidoreductase subunit A10) The protein encoded by this gene is a component of 42 kDa complex I, the first enzyme complex in the electron transport chain of mitochondria. This protein has NADH dehydrogenase activity and oxidoreductase activity. It transfers electrons from NADH to the respiratory chain. A mutation in this gene was found in an individual with Leigh syndrome. [provided by RefSeq, Apr 2016]

NDUFA10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDUFA10	NR_136158.2 linkuse as main transcript	n.3974-8687_3974-8647del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
NDUFA10	ENST00000419408.5 linkuse as main transcript	c.295-26363_295-26323del	intron_variant	5
NDUFA10	ENST00000679183.1 linkuse as main transcript	c.1000-8687_1000-8647del	intron_variant, NMD_transcript_variant
NDUFA10	ENST00000677057.1 linkuse as main transcript	n.4029-8687_4029-8647del	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0611

AC:

9290

AN:

152086

Hom.:

363

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0240

Gnomad AMI

AF:

0.0954

Gnomad AMR

AF:

0.0472

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.105

Gnomad SAS

AF:

0.0802

Gnomad FIN

AF:

0.0855

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0750

Gnomad OTH

AF:

0.0664

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

GnomAD4 genome

AF:

0.0611

AC:

9296

AN:

152204

Hom.:

362

Cov.:

AF XY:

0.0612

AC XY:

4557

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0242

Gnomad4 AMR

AF:

0.0471

Gnomad4 ASJ

AF:

0.111

Gnomad4 EAS

AF:

0.105

Gnomad4 SAS

AF:

0.0807

Gnomad4 FIN

AF:

0.0855

Gnomad4 NFE

AF:

0.0750

Gnomad4 OTH

AF:

0.0662

Alfa

AF:

0.0545

Hom.:

Asia WGS

AF:

0.0850

AC:

296

AN:

3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Schizophrenia

Uncertain:1

Uncertain significance, no assertion criteria provided

case-control

Department of Psychiatry, The University of Hong Kong

Nov 11, 2022

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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