6-32706872-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.571 AC: 330 AN: 578

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.561 AC: 23184 AN: 41334

American (AMR) AF: 0.643 AC: 9808 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2613 AN: 3468

East Asian (EAS) AF: 0.729 AC: 3758 AN: 5156

South Asian (SAS) AF: 0.667 AC: 3212 AN: 4818

European-Finnish (FIN) AF: 0.541 AC: 5697 AN: 10536

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.574 AC: 38953 AN: 67874

Other (OTH) AF: 0.641 AC: 1349 AN: 2106

Alfa AF: 0.579 Hom.: 9663

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
PhyloP100		-5.3

Splicing

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

Other links and lift over

dbSNP: rs9275517; hg19: chr6-32674649;