10-100529321-C-G

Variant names:

• chr10-100529321-C-G
• rs1800662
• NM_005004.4:c.212+59G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005004.4(NDUFB8):​c.212+59G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000742 in 1,348,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 28)
  • Exomes 𝑓: 7.4e-7 (0 hom.)
• Consequence: NDUFB8 NM_005004.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 0 publications found

Genes affected

NDUFB8 (HGNC:7703): (NADH:ubiquinone oxidoreductase subunit B8) Involved in mitochondrial respiratory chain complex I assembly. Located in endoplasmic reticulum and mitochondrion. Part of mitochondrial respiratory chain complex I. Implicated in nuclear type mitochondrial complex I deficiency 32. Biomarker of Alzheimer's disease and Parkinson's disease. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000255339 (HGNC:):

HIF1AN (HGNC:17113): (hypoxia inducible factor 1 subunit alpha inhibitor) Enables several functions, including 2-oxoglutarate-dependent dioxygenase activity; NF-kappaB binding activity; and transition metal ion binding activity. Involved in several processes, including negative regulation of Notch signaling pathway; negative regulation of transcription from RNA polymerase II promoter in response to hypoxia; and protein hydroxylation. Located in cytosol; nucleoplasm; and perinuclear region of cytoplasm. Colocalizes with nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFB8	NM_005004.4	c.212+59G>C		intron_variant	Intron 2 of 4	ENST00000299166.9	NP_004995.1
NDUFB8	NM_001284367.2	c.212+59G>C		intron_variant	Intron 2 of 4		NP_001271296.1
NDUFB8	NM_001284368.1	c.119+59G>C		intron_variant	Intron 2 of 4		NP_001271297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDUFB8	ENST00000299166.9	c.212+59G>C		intron_variant	Intron 2 of 4	1	NM_005004.4	ENSP00000299166.4
ENSG00000255339	ENST00000557395.5	n.212+59G>C		intron_variant	Intron 2 of 9	2		ENSP00000456832.1

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome AF: 7.42e-7 AC: 1 AN: 1348168 Hom.: 0 Cov.: 30 AF XY: 0.00000151 AC XY: 1 AN XY: 663994

African (AFR) AF: 0.00 AC: 0 AN: 27662

American (AMR) AF: 0.00 AC: 0 AN: 25400

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21540

East Asian (EAS) AF: 0.00 AC: 0 AN: 33158

South Asian (SAS) AF: 0.00 AC: 0 AN: 70860

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51036

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5396

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1057922

Other (OTH) AF: 0.0000181 AC: 1 AN: 55194

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.7
DANN	Benign	0.80
PhyloP100		-0.42
PromoterAI		0.042	Neutral

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: rs1800662; hg19: chr10-102289078;