rs132671

Variant names:

• chr22-36173796-A-G
• rs132671
• ENST00000437339.1:n.521A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-36173796-A-G
• chr22-36173796-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MTCO2P20		n.36173796A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTCO2P20	ENST00000437339.1	n.521A>G		non_coding_transcript_exon_variant	Exon 2 of 2	6

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

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.581 AC: 24062 AN: 41412

American (AMR) AF: 0.665 AC: 10157 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2636 AN: 3472

East Asian (EAS) AF: 0.922 AC: 4772 AN: 5174

South Asian (SAS) AF: 0.840 AC: 4041 AN: 4812

European-Finnish (FIN) AF: 0.684 AC: 7213 AN: 10546

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41985 AN: 67970

Other (OTH) AF: 0.653 AC: 1377 AN: 2110

Alfa AF: 0.640 Hom.: 11941

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
PhyloP100		5.1

Splicing

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

Other links and lift over

dbSNP: rs132671; hg19: chr22-36569844;