22-42132969-C-T

Position:

• chr22-42132969-C-T

Variant summary

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

The ENST00000417586.1(ENSG00000227370):​n.427C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 155,106 control chromosomes in the GnomAD database, including 5,004 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 0.22 (4819 hom., cov: 32)
  • Exomes 𝑓: 0.22 (185 hom.)
• Consequence: ENSG00000227370 ENST00000417586.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

Genes affected

ENSG00000227370 (HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000227370	ENST00000417586.1	n.427C>T		non_coding_transcript_exon_variant	1/1	6
NDUFA6-DT	ENST00000439129.5	n.1719-3230C>T		intron_variant		5
NDUFA6-DT	ENST00000617009.4	n.394-71C>T		intron_variant		5
NDUFA6-DT	ENST00000621190.1	n.394-71C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32719 AN: 150510 Hom.: 4820 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.224 AC: 1005 AN: 4482 Hom.: 185 Cov.: 0 AF XY: 0.232 AC XY: 561 AN XY: 2414

Gnomad4 AFR exome AF: 0.209

Gnomad4 AMR exome AF: 0.186

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.737

Gnomad4 SAS exome AF: 0.162

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.289

Gnomad4 OTH exome AF: 0.244

GnomAD4 genome AF: 0.217 AC: 32717 AN: 150624 Hom.: 4819 Cov.: 32 AF XY: 0.211 AC XY: 15522 AN XY: 73548

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.196

Alfa AF: 0.218 Hom.: 1053

Bravo AF: 0.224

Asia WGS AF: 0.294 AC: 1020 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28360521; hg19: chr22-42528976;