rs1878553

Variant names:

• chr18-2570156-C-T
• rs1878553
• NM_022840.5:c.-439+993G>A

Variant summary

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

The NM_022840.5(METTL4):​c.-439+993G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,096 control chromosomes in the GnomAD database, including 4,844 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 0.24 (4844 hom., cov: 32)
• Consequence: METTL4 NM_022840.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 4 publications found

Genes affected

METTL4 (HGNC:24726): (methyltransferase 4, N6-adenosine) Enables RNA methyltransferase activity and site-specific DNA-methyltransferase (adenine-specific) activity. Involved in nucleic acid metabolic process; regulation of RNA metabolic process; and regulation of mitochondrial DNA replication. Located in cytosol; mitochondrial matrix; and nucleus. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022840.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	METTL4	NM_022840.5	MANE Select	c.-439+993G>A		intron	N/A	NP_073751.3
	METTL4	NM_001308401.2		c.-439+993G>A		intron	N/A	NP_001295330.1	J3KNJ7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	METTL4	ENST00000574538.2	TSL:1 MANE Select	c.-439+993G>A		intron	N/A	ENSP00000458290.1	Q8N3J2
	METTL4	ENST00000919555.1		c.-439+993G>A		intron	N/A	ENSP00000589614.1
	METTL4	ENST00000919556.1		c.-439+993G>A		intron	N/A	ENSP00000589615.1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37167 AN: 151978 Hom.: 4843 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0554

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.245 AC: 37195 AN: 152096 Hom.: 4844 Cov.: 32 AF XY: 0.241 AC XY: 17915 AN XY: 74362

African (AFR) AF: 0.315 AC: 13054 AN: 41436

American (AMR) AF: 0.188 AC: 2877 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3470

East Asian (EAS) AF: 0.0555 AC: 288 AN: 5190

South Asian (SAS) AF: 0.148 AC: 714 AN: 4822

European-Finnish (FIN) AF: 0.244 AC: 2580 AN: 10570

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16505 AN: 67990

Other (OTH) AF: 0.225 AC: 476 AN: 2112

Alfa AF: 0.234 Hom.: 7912

Bravo AF: 0.241

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.43
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1878553; hg19: chr18-2570155;