rs5758589

chr22-42122378-A-G

Variant summary

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

The NR_034118.2(NDUFA6-DT):n.668-1669A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,044 control chromosomes in the GnomAD database, including 26,899 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 0.59 (26899 hom., cov: 32)
• Consequence: NDUFA6-DT NR_034118.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

Genes affected

NDUFA6-DT (HGNC:45273): (NDUFA6 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDUFA6-DT	NR_034118.2	n.668-1669A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDUFA6-DT	ENST00000439129.5	n.670-1669A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89355 AN: 151926 Hom.: 26861 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.588 AC: 89441 AN: 152044 Hom.: 26899 Cov.: 32 AF XY: 0.584 AC XY: 43446 AN XY: 74334

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.564

Alfa AF: 0.559 Hom.: 15891

Bravo AF: 0.590

Asia WGS AF: 0.572 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.34
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5758589; hg19: chr22-42518382;