22-42132027-CTTTTTTTTTTTTT-CT

Position:

• chr22-42132027-CTTTTTTTTTTTTT-CT

Variant summary

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

The ENST00000617009.4(NDUFA6-DT):​n.-3_9delTTTTTTTTTTTT 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 0.0000163 in 122,464 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 0.000016 (0 hom., cov: 27)
• Consequence: NDUFA6-DT ENST00000617009.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

Genes affected

NDUFA6-DT (HGNC:):

ACMG classification

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
		n.42132028_42132039delTTTTTTTTTTTT		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDUFA6-DT	ENST00000617009.4	n.-3_9delTTTTTTTTTTTT		non_coding_transcript_exon_variant	1/5	5
NDUFA6-DT	ENST00000621190.1	n.-3_9delTTTTTTTTTTTT		non_coding_transcript_exon_variant	1/8	5
NDUFA6-DT	ENST00000439129.5	n.1719-4171_1719-4160delTTTTTTTTTTTT		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0000163 AC: 2 AN: 122478 Hom.: 0 Cov.: 27

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000308

Gnomad EAS AF: 0.000224

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000163 AC: 2 AN: 122464 Hom.: 0 Cov.: 27 AF XY: 0.0000174 AC XY: 1 AN XY: 57492

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000308

Gnomad4 EAS AF: 0.000225

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000264

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: -;