ENST00000422088.1:n.84T>C

Variant names:

• chr6-32706872-A-G
• rs9275517
• ENST00000422088.1:n.84T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422088.1(MTCO3P1):​n.84T>C 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 0.589 in 151,750 control chromosomes in the GnomAD database, including 26,726 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 0.59 (26726 hom., cov: 31)
  • Exomes 𝑓: 0.57 (102 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTCO3P1 ENST00000422088.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.34

Genes affected

MTCO3P1 (HGNC:31342): (MT-CO3 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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
MTCO3P1	ENST00000422088.1	n.84T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89380 AN: 151632 Hom.: 26719 Cov.: 31

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.639

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.572 AC: 335 AN: 586 Hom.: 102 Cov.: 0 AF XY: 0.563 AC XY: 187 AN XY: 332

Gnomad4 FIN exome AF: 0.571

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.589 AC: 89435 AN: 151750 Hom.: 26726 Cov.: 31 AF XY: 0.589 AC XY: 43731 AN XY: 74186

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.641

Alfa AF: 0.571 Hom.: 3650

Bravo AF: 0.599

Asia WGS AF: 0.719 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	1.4
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275517; hg19: chr6-32674649;