6-32706960-C-G

Variant names:

• chr6-32706960-C-G
• rs1794265
• ENST00000422088.1:n.-5G>C

Variant summary

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

The ENST00000422088.1(MTCO3P1):​n.-5G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0227 in 152,254 control chromosomes in the GnomAD database, including 59 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 0.023 (59 hom., cov: 32)
  • Exomes 𝑓: 0.0078 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTCO3P1 ENST00000422088.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0774 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.-5G>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0227 AC: 3451 AN: 152136 Hom.: 59 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.0837

Gnomad FIN AF: 0.00858

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0279

Gnomad OTH AF: 0.0234

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00781 AC: 1 AN: 128 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 68

Gnomad4 FIN exome AF: 0.00820

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0227 AC: 3454 AN: 152254 Hom.: 59 Cov.: 32 AF XY: 0.0226 AC XY: 1682 AN XY: 74448

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.0179

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.0397

Gnomad4 SAS AF: 0.0842

Gnomad4 FIN AF: 0.00858

Gnomad4 NFE AF: 0.0279

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.00995 Hom.: 4

Bravo AF: 0.0213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	9.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1794265; hg19: chr6-32674737;