22-42132561-C-T

Variant names:

• chr22-42132561-C-T
• rs1080983
• ENST00000417586.1:n.19C>T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000617009.4(NDUFA6-DT):​n.352C>T 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 0.275 in 150,752 control chromosomes in the GnomAD database, including 7,283 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.27 (7274 hom., cov: 32)
  • Exomes 𝑓: 0.25 (9 hom.)
• Consequence: NDUFA6-DT ENST00000617009.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

Genes affected

ENSG00000227370 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 22-42132561-C-T is Benign according to our data. Variant chr22-42132561-C-T is described in Lovd as [Likely_benign]. Variant chr22-42132561-C-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

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
ENSG00000227370	ENST00000417586.1	n.19C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
NDUFA6-DT	ENST00000617009.4	n.352C>T		non_coding_transcript_exon_variant	Exon 2 of 5	5
NDUFA6-DT	ENST00000621190.1	n.352C>T		non_coding_transcript_exon_variant	Exon 2 of 8	5
NDUFA6-DT	ENST00000439129.5	n.1719-3638C>T		intron_variant	Intron 5 of 6	5

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41377 AN: 150466 Hom.: 7264 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.306

GnomAD4 exome AF: 0.250 AC: 43 AN: 172 Hom.: 9 Cov.: 0 AF XY: 0.234 AC XY: 30 AN XY: 128

Gnomad4 AFR exome AF: 0.333

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.297

Gnomad4 OTH exome AF: 0.0625

GnomAD4 genome AF: 0.275 AC: 41402 AN: 150580 Hom.: 7274 Cov.: 32 AF XY: 0.281 AC XY: 20631 AN XY: 73538

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.304

Alfa AF: 0.309 Hom.: 2024

Bravo AF: 0.261

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1080983; hg19: chr22-42528568;