12-57771302-C-T

Variant summary

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

The NM_005371.6(METTL1):c.111-45G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 1,476,274 control chromosomes in the GnomAD database, including 101,673 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 0.33 (8550 hom., cov: 32)
  • Exomes 𝑓: 0.38 (93123 hom.)
• Consequence: METTL1 NM_005371.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

METTL1 (HGNC:7030): (methyltransferase 1, tRNA methylguanosine) This gene is similar in sequence to the S. cerevisiae YDL201w gene. The gene product contains a conserved S-adenosylmethionine-binding motif and is inactivated by phosphorylation. Alternative splice variants encoding different protein isoforms have been described for this gene. A pseudogene has been identified on chromosome X. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
METTL1	NM_005371.6	c.111-45G>A		intron_variant		ENST00000324871.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
METTL1	ENST00000324871.12	c.111-45G>A		intron_variant		1	NM_005371.6	P1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49191 AN: 150026 Hom.: 8524 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.277

GnomAD3 exomes AF: 0.381 AC: 90365 AN: 237072 Hom.: 18819 AF XY: 0.388 AC XY: 49534 AN XY: 127712

Gnomad AFR exome AF: 0.276

Gnomad AMR exome AF: 0.360

Gnomad ASJ exome AF: 0.278

Gnomad EAS exome AF: 0.651

Gnomad SAS exome AF: 0.560

Gnomad FIN exome AF: 0.365

Gnomad NFE exome AF: 0.325

Gnomad OTH exome AF: 0.328

GnomAD4 exome AF: 0.378 AC: 501516 AN: 1326124 Hom.: 93123 Cov.: 28 AF XY: 0.384 AC XY: 252902 AN XY: 659168

Gnomad4 AFR exome AF: 0.292

Gnomad4 AMR exome AF: 0.370

Gnomad4 ASJ exome AF: 0.331

Gnomad4 EAS exome AF: 0.730

Gnomad4 SAS exome AF: 0.550

Gnomad4 FIN exome AF: 0.407

Gnomad4 NFE exome AF: 0.354

Gnomad4 OTH exome AF: 0.384

GnomAD4 genome AF: 0.328 AC: 49266 AN: 150150 Hom.: 8550 Cov.: 32 AF XY: 0.336 AC XY: 24662 AN XY: 73348

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.284

Alfa AF: 0.316 Hom.: 11005

Bravo AF: 0.312

Asia WGS AF: 0.602 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	9.8
Dann	Benign	0.54

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

Publications

LitVar

Other links and lift over

dbSNP: rs10877013; hg19: chr12-58165085;