22-36173796-A-G

Position:

• chr22-36173796-A-G

Variant summary

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

The ENST00000437339.1(MTCO2P20):​n.521A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.638 in 151,988 control chromosomes in the GnomAD database, including 31,517 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 0.64 (31516 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: MTCO2P20 ENST00000437339.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.08

Genes affected

MTCO2P20 (HGNC:52149): (MT-CO2 pseudogene 20)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTCO2P20	ENST00000437339.1	n.521A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96931 AN: 151868 Hom.: 31489 Cov.: 31

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.651

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.638 AC: 97007 AN: 151986 Hom.: 31516 Cov.: 31 AF XY: 0.648 AC XY: 48120 AN XY: 74290

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.653

Alfa AF: 0.621 Hom.: 6149

Bravo AF: 0.632

Asia WGS AF: 0.826 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	0.75
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs132671; hg19: chr22-36569844;