chr22-42132027-CTT-C

Variant names:

• chr22-42132027-CTT-C
• rs267608321
• ENST00000439129.5:n.1719-4171_1719-4170delTT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000439129.5(NDUFA6-DT):​n.1719-4171_1719-4170delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000825 in 122,436 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00082 (2 hom., cov: 27)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NDUFA6-DT ENST00000439129.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 0 publications found

Genes affected

NDUFA6-DT (HGNC:45273): (NDUFA6 divergent transcript)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDUFA6-DT	ENST00000439129.5	n.1719-4171_1719-4170delTT		intron_variant	Intron 5 of 6	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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000414 AC: 13 AN: 31392

American (AMR) AF: 0.000700 AC: 8 AN: 11432

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3244

East Asian (EAS) AF: 0.000449 AC: 2 AN: 4450

South Asian (SAS) AF: 0.00 AC: 0 AN: 3868

European-Finnish (FIN) AF: 0.00102 AC: 5 AN: 4898

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 232

European-Non Finnish (NFE) AF: 0.000877 AC: 53 AN: 60440

Other (OTH) AF: 0.00178 AC: 3 AN: 1684

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs267608321; hg19: -;