NM_005005.3:c.101+240G>C

Variant names:

• chr8-124539527-G-C
• rs7011005
• NM_005005.3:c.101+240G>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_005005.3(NDUFB9):​c.101+240G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0042 in 544,148 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.011 (28 hom., cov: 33)
  • Exomes 𝑓: 0.0015 (8 hom.)
• Consequence: NDUFB9 NM_005005.3 intron
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.142
• Publications: 0 publications found

Genes affected

NDUFB9 (HGNC:7704): (NADH:ubiquinone oxidoreductase subunit B9) The protein encoded by this gene is a subunit of the mitochondrial oxidative phosphorylation complex I (nicotinamide adenine dinucleotide: ubiquinone oxidoreductase). Complex I is localized to the inner mitochondrial membrane and functions to dehydrogenate nicotinamide adenine dinucleotide and to shuttle electrons to coenzyme Q. Complex I deficiency is the most common defect found in oxidative phosphorylation disorders and results in a range of conditions, including lethal neonatal disease, hypertrophic cardiomyopathy, liver disease, and adult-onset neurodegenerative disorders. Pseudogenes of this gene are found on chromosomes five, seven and eight. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

TATDN1 (HGNC:24220): (TatD DNase domain containing 1) Predicted to enable 3'-5'-exodeoxyribonuclease activity. Predicted to be involved in DNA metabolic process and nucleic acid phosphodiester bond hydrolysis. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 8-124539527-G-C is Benign according to our data. Variant chr8-124539527-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1316727.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0112 (1703/152326) while in subpopulation AFR AF = 0.0385 (1601/41572). AF 95% confidence interval is 0.0369. There are 28 homozygotes in GnomAd4. There are 831 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 28 AR,Unknown gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFB9	NM_005005.3	c.101+240G>C		intron_variant	Intron 1 of 3	ENST00000276689.8	NP_004996.1
NDUFB9	NM_001311168.2	c.101+240G>C		intron_variant	Intron 1 of 3		NP_001298097.1
NDUFB9	NM_001278646.2	c.-27+240G>C		intron_variant	Intron 1 of 3		NP_001265575.1
NDUFB9	NM_001278645.2	c.-33+240G>C		intron_variant	Intron 1 of 3		NP_001265574.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDUFB9	ENST00000276689.8	c.101+240G>C		intron_variant	Intron 1 of 3	1	NM_005005.3	ENSP00000276689.3

Frequencies

GnomAD3 genomes AF: 0.0111 AC: 1697 AN: 152208 Hom.: 28 Cov.: 33

Gnomad AFR AF: 0.0385

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00477

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000191

Gnomad OTH AF: 0.00718

GnomAD4 exome AF: 0.00148 AC: 581 AN: 391822 Hom.: 8 AF XY: 0.00131 AC XY: 270 AN XY: 205568

African (AFR) AF: 0.0384 AC: 432 AN: 11254

American (AMR) AF: 0.00222 AC: 37 AN: 16690

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12026

East Asian (EAS) AF: 0.00 AC: 0 AN: 26016

South Asian (SAS) AF: 0.000236 AC: 10 AN: 42368

European-Finnish (FIN) AF: 0.0000408 AC: 1 AN: 24484

Middle Eastern (MID) AF: 0.00353 AC: 6 AN: 1698

European-Non Finnish (NFE) AF: 0.0000896 AC: 21 AN: 234482

Other (OTH) AF: 0.00325 AC: 74 AN: 22804

GnomAD4 genome AF: 0.0112 AC: 1703 AN: 152326 Hom.: 28 Cov.: 33 AF XY: 0.0112 AC XY: 831 AN XY: 74500

African (AFR) AF: 0.0385 AC: 1601 AN: 41572

American (AMR) AF: 0.00477 AC: 73 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000191 AC: 13 AN: 68026

Other (OTH) AF: 0.00710 AC: 15 AN: 2112

Alfa AF: 0.00798 Hom.: 1

Bravo AF: 0.0131

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 07, 2018

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.43
PhyloP100		-0.14
PromoterAI		-0.062	Neutral
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs7011005; hg19: chr8-125551768;