chr22-42132027-C-CT

Position:

• chr22-42132027-C-CT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.027 in 121,848 control chromosomes in the GnomAD database, including 144 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.027 (144 hom., cov: 27)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.062 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.42132027_42132028insT		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDUFA6-DT	ENST00000439129.5	n.1719-4172_1719-4171insT		intron_variant		5
NDUFA6-DT	ENST00000617009.4	n.-4_-3insT		upstream_gene_variant		5
NDUFA6-DT	ENST00000621190.1	n.-4_-3insT		upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 3287 AN: 121852 Hom.: 144 Cov.: 27

Gnomad AFR AF: 0.0643

Gnomad AMI AF: 0.00496

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.0146

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.00565

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0232

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0270 AC: 3288 AN: 121844 Hom.: 144 Cov.: 27 AF XY: 0.0258 AC XY: 1473 AN XY: 57198

Gnomad4 AFR AF: 0.0643

Gnomad4 AMR AF: 0.0149

Gnomad4 ASJ AF: 0.0146

Gnomad4 EAS AF: 0.0286

Gnomad4 SAS AF: 0.00569

Gnomad4 FIN AF: 0.0123

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.0232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs267608321; hg19: -;