ENST00000417586.1:n.19C>T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.27 (7274 hom., cov: 32)
  • Exomes 𝑓: 0.25 (9 hom.)
• Consequence: ENSG00000227370 ENST00000417586.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 23 publications found

Genes affected

ENSG00000227370 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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

African (AFR) AF: 0.333 AC: 2 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 14

South Asian (SAS) AF: 0.00 AC: 0 AN: 6

European-Finnish (FIN) AF: 0.400 AC: 4 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.297 AC: 35 AN: 118

Other (OTH) AF: 0.0625 AC: 1 AN: 16

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

African (AFR) AF: 0.139 AC: 5666 AN: 40794

American (AMR) AF: 0.300 AC: 4553 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3462

East Asian (EAS) AF: 0.148 AC: 755 AN: 5110

South Asian (SAS) AF: 0.383 AC: 1819 AN: 4746

European-Finnish (FIN) AF: 0.389 AC: 4087 AN: 10498

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.331 AC: 22357 AN: 67500

Other (OTH) AF: 0.304 AC: 633 AN: 2084

Alfa AF: 0.268 Hom.: 2288

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
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1080983; hg19: chr22-42528568;