Variant 19-5892812-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001193375.3(NDUFA11):c.*105C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00989 in 1,339,710 control chromosomes in the GnomAD database, including 152 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.016 ( 33 hom., cov: 33)

Exomes 𝑓: 0.0091 ( 119 hom. )

Consequence

NDUFA11
NM_001193375.3 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.836

Variant links:

Genes affected

NDUFA11 (HGNC:20371): (NADH:ubiquinone oxidoreductase subunit A11) This gene encodes a subunit of the membrane-bound mitochondrial complex I. Complex I is composed of numerous subunits and functions as the NADH-ubiquinol reductase of the mitochondrial electron transport chain. Mutations in this gene are associated with severe mitochondrial complex I deficiency. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2010]

NDUFA11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 19-5892812-G-C is Benign according to our data. Variant chr19-5892812-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1318064.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0162 (2463/152316) while in subpopulation SAS AF= 0.0396 (191/4828). AF 95% confidence interval is 0.0358. There are 33 homozygotes in gnomad4. There are 1198 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 33 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDUFA11	NM_001193375.3 linkuse as main transcript	c.*105C>G		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDUFA11	ENST00000418389.6 linkuse as main transcript	c.*105C>G		3_prime_UTR_variant	4/4	2			Q86Y39-2

Frequencies

GnomAD3 genomes

AF:

0.0161

AC:

2456

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0373

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00576

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0393

Gnomad FIN

AF:

0.00433

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00794

Gnomad OTH

AF:

0.0163

GnomAD4 exome

AF:

0.00908

AC:

10784

AN:

1187394

Hom.:

119

Cov.:

AF XY:

0.00957

AC XY:

5471

AN XY:

571956

show subpopulations

Gnomad4 AFR exome

AF:

0.0405

Gnomad4 AMR exome

AF:

0.00530

Gnomad4 ASJ exome

AF:

0.00116

Gnomad4 EAS exome

AF:

0.000120

Gnomad4 SAS exome

AF:

0.0425

Gnomad4 FIN exome

AF:

0.00578

Gnomad4 NFE exome

AF:

0.00712

Gnomad4 OTH exome

AF:

0.0105

GnomAD4 genome

AF:

0.0162

AC:

2463

AN:

152316

Hom.:

Cov.:

AF XY:

0.0161

AC XY:

1198

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0374

Gnomad4 AMR

AF:

0.00569

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0396

Gnomad4 FIN

AF:

0.00433

Gnomad4 NFE

AF:

0.00794

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.0132

Hom.:

Bravo

AF:

0.0163

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.30

DANN

Benign

0.40

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