ENST00000532947.2:n.*425-37925G>A

Variant names:

• chr11-28488553-G-A
• rs2582905
• ENST00000532947.2:n.*425-37925G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532947.2(METTL15):​n.*425-37925G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,994 control chromosomes in the GnomAD database, including 27,509 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 (27509 hom., cov: 32)
• Consequence: METTL15 ENST00000532947.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 8 publications found

Genes affected

METTL15 (HGNC:26606): (methyltransferase 15, mitochondrial 12S rRNA N4-cytidine) Predicted to enable rRNA (cytosine-N4-)-methyltransferase activity. Predicted to be involved in rRNA base methylation. Predicted to be located in mitochondrial matrix. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532947.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	METTL15	ENST00000532947.2	TSL:5	n.*425-37925G>A		intron	N/A	ENSP00000489497.1

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88905 AN: 151876 Hom.: 27482 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.551

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.585 AC: 88977 AN: 151994 Hom.: 27509 Cov.: 32 AF XY: 0.589 AC XY: 43719 AN XY: 74266

African (AFR) AF: 0.787 AC: 32649 AN: 41504

American (AMR) AF: 0.475 AC: 7248 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1813 AN: 3470

East Asian (EAS) AF: 0.736 AC: 3806 AN: 5170

South Asian (SAS) AF: 0.645 AC: 3104 AN: 4812

European-Finnish (FIN) AF: 0.500 AC: 5265 AN: 10540

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33384 AN: 67930

Other (OTH) AF: 0.546 AC: 1154 AN: 2112

Alfa AF: 0.514 Hom.: 25350

Bravo AF: 0.589

Asia WGS AF: 0.629 AC: 2188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	2.2
DANN	Benign	0.86
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2582905; hg19: chr11-28510100;