22-42132027-CTT-C

Position:

• chr22-42132027-CTT-C

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6 BS2

The variant allele was found at a frequency of 0.000825 in 122,436 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.00082 (2 hom., cov: 27)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP6: Variant 22-42132027-CTT-C is Benign according to our data. Variant chr22-42132027-CTT-C is described in Lovd as [Likely_benign]. Variant chr22-42132027-CTT-C is described in Lovd as [Likely_benign].
• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.42132028_42132029delTT		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDUFA6-DT	ENST00000439129.5	n.1719-4171_1719-4170delTT		intron_variant		5
NDUFA6-DT	ENST00000617009.4	n.-3_-2delTT		upstream_gene_variant		5
NDUFA6-DT	ENST00000621190.1	n.-3_-2delTT		upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.000825 AC: 101 AN: 122450 Hom.: 2 Cov.: 27

Gnomad AFR AF: 0.000415

Gnomad AMI AF: 0.0214

Gnomad AMR AF: 0.000700

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000448

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00102

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000877

Gnomad OTH AF: 0.00179

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.000825 AC: 101 AN: 122436 Hom.: 2 Cov.: 27 AF XY: 0.000905 AC XY: 52 AN XY: 57482

Gnomad4 AFR AF: 0.000414

Gnomad4 AMR AF: 0.000700

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000449

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00102

Gnomad4 NFE AF: 0.000877

Gnomad4 OTH AF: 0.00178

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: -;