6-32706872-A-G

Position:

• chr6-32706872-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTCO3P1	ENST00000422088.1	n.84T>C		non_coding_transcript_exon_variant	1/1

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;