rs1080983

chr22-42132561-C-T

Variant summary

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

The ENST00000417586.1(ENSG00000227370):n.19C>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: ENST00000417586.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000417586.1	n.19C>T		non_coding_transcript_exon_variant	1/1
NDUFA6-DT	ENST00000439129.5	n.1719-3638C>T		intron_variant, non_coding_transcript_variant		5
NDUFA6-DT	ENST00000617009.4	n.352C>T		non_coding_transcript_exon_variant	2/5	5
NDUFA6-DT	ENST00000621190.1	n.352C>T		non_coding_transcript_exon_variant	2/8	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;