Variant 22-42132027-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The variant allele was found at a frequency of 0.00000816 in 122,474 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000082 ( 0 hom., cov: 27)

Consequence

intergenic_region

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.42132027_42132028insTTTTTTTT		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
NDUFA6-DT	ENST00000439129.5 linkuse as main transcript	n.1719-4172_1719-4171insTTTTTTTT	intron_variant	5
NDUFA6-DT	ENST00000617009.4 linkuse as main transcript	n.-4_-3insTTTTTTTT	upstream_gene_variant	5
NDUFA6-DT	ENST00000621190.1 linkuse as main transcript	n.-4_-3insTTTTTTTT	upstream_gene_variant	5

Frequencies

GnomAD3 genomes

AF:

0.00000817

AC:

AN:

122474

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000204

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

AF:

0.00000817

AC:

AN:

122474

Hom.:

Cov.:

AF XY:

0.0000174

AC XY:

AN XY:

57466

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000204

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over