X-47142212-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000687244.1(NDUFB11):c.*105G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00613 in 1,065,501 control chromosomes in the GnomAD database, including 259 homozygotes. There are 1,653 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.030 (154 hom., 854 hem., cov: 22)
  • Exomes 𝑓: 0.0033 (105 hom. 799 hem.)
• Consequence: NDUFB11 ENST00000687244.1 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.145

Genes affected

NDUFB11 (HGNC:20372): (NADH:ubiquinone oxidoreductase subunit B11) The protein encoded by this gene is a subunit of the multisubunit NADH:ubiquinone oxidoreductase (complex I). Mammalian complex I is located at the mitochondrial inner membrane. This protein has NADH dehydrogenase activity and oxidoreductase activity. It transfers electrons from NADH to ubiquinone. Mutations in the human gene are associated with linear skin defects with multiple congenital anomalies 3 and mitochondrial complex I deficiency. [provided by RefSeq, Dec 2016]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant X-47142212-C-T is Benign according to our data. Variant chrX-47142212-C-T is described in ClinVar as [Benign]. Clinvar id is 1284247.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDUFB11	NM_001135998.3			downstream_gene_variant		ENST00000377811.4
NDUFB11	NM_019056.7			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDUFB11	ENST00000377811.4			downstream_gene_variant		1	NM_001135998.3	P1

Frequencies

GnomAD3 genomes AF: 0.0303 AC: 3388 AN: 111687 Hom.: 152 Cov.: 22 AF XY: 0.0251 AC XY: 851 AN XY: 33869

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0106

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00840

Gnomad NFE AF: 0.000564

Gnomad OTH AF: 0.0267

GnomAD4 exome AF: 0.00329 AC: 3138 AN: 953761 Hom.: 105 Cov.: 17 AF XY: 0.00285 AC XY: 799 AN XY: 280667

Gnomad4 AFR exome AF: 0.108

Gnomad4 AMR exome AF: 0.00649

Gnomad4 ASJ exome AF: 0.0000621

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000254

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000165

Gnomad4 OTH exome AF: 0.00813

GnomAD4 genome AF: 0.0304 AC: 3394 AN: 111740 Hom.: 154 Cov.: 22 AF XY: 0.0252 AC XY: 854 AN XY: 33932

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0105

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000564

Gnomad4 OTH AF: 0.0263

Alfa AF: 0.0172 Hom.: 73

Bravo AF: 0.0348

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.7
Dann	Benign	0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs73630256; hg19: chrX-47001611;