rs2582905

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
METTL15	XR_007062458.1	n.1414-37925G>A		intron_variant	Intron 10 of 11
METTL15	XR_930849.3	n.1332-37925G>A		intron_variant	Intron 9 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
METTL15	ENST00000532947.2	n.*425-37925G>A		intron_variant	Intron 6 of 7	5		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 v4.3

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;