rs16917360

Variant names:

• chr8-95114904-G-A
• rs16917360
• ENST00000523184.5:n.345-632G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-95114904-G-A
• chr8-95114904-G-C
• chr8-95114904-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000523184.5(NDUFAF6):​n.345-632G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 152,126 control chromosomes in the GnomAD database, including 170 homozygotes. 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: 𝑓 0.045 (170 hom., cov: 31)
• Consequence: NDUFAF6 ENST00000523184.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.773

Genes affected

NDUFAF6 (HGNC:28625): (NADH:ubiquinone oxidoreductase complex assembly factor 6) This gene encodes a protein that localizes to mitochondria and contains a predicted phytoene synthase domain. The encoded protein plays an important role in the assembly of complex I (NADH-ubiquinone oxidoreductase) of the mitochondrial respiratory chain through regulation of subunit ND1 biogenesis. Mutations in this gene are associated with complex I enzymatic deficiency. [provided by RefSeq, Nov 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFAF6	NR_148913.2	n.1067-632G>A		intron_variant	Intron 9 of 10
NDUFAF6	NR_148914.2	n.1264-632G>A		intron_variant	Intron 10 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDUFAF6	ENST00000523184.5	n.345-632G>A		intron_variant	Intron 4 of 5	3

Frequencies

GnomAD3 genomes AF: 0.0452 AC: 6867 AN: 152008 Hom.: 170 Cov.: 31

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.0175

Gnomad SAS AF: 0.0719

Gnomad FIN AF: 0.0534

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0588

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0451 AC: 6864 AN: 152126 Hom.: 170 Cov.: 31 AF XY: 0.0448 AC XY: 3331 AN XY: 74380

Gnomad4 AFR AF: 0.0152

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.0433

Gnomad4 EAS AF: 0.0178

Gnomad4 SAS AF: 0.0719

Gnomad4 FIN AF: 0.0534

Gnomad4 NFE AF: 0.0588

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0542 Hom.: 344

Bravo AF: 0.0427

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16917360; hg19: chr8-96127132;