Variant 7-128500928-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000262432.13(METTL2B):c.942T>C(p.Tyr314Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 1,612,724 control chromosomes in the GnomAD database, including 127,862 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 11566 hom., cov: 32)

Exomes 𝑓: 0.40 ( 116296 hom. )

Consequence

METTL2B
ENST00000262432.13 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.00200

Variant links:

Genes affected

METTL2B (HGNC:18272): (methyltransferase 2B, tRNA N3-cytidine) This gene is a member of a family of methyltransferases that share homology with, but are distinct from, the UbiE family of methyltransferases. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

METTL2B links:

METTL2B (HGNC:):

METTL2B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 7-128500928-T-C is Benign according to our data. Variant chr7-128500928-T-C is described in ClinVar as [Benign]. Clinvar id is 768200.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.002 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
METTL2B	NM_018396.3 linkuse as main transcript	c.942T>C	p.Tyr314Tyr	synonymous_variant	8/9	ENST00000262432.13	NP_060866.2	Q6P1Q9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
METTL2B	ENST00000262432.13 linkuse as main transcript	c.942T>C	p.Tyr314Tyr	synonymous_variant	8/9	1	NM_018396.3	ENSP00000262432.9	Q6P1Q9-1
METTL2B	ENST00000482555.5 linkuse as main transcript	n.1185T>C		non_coding_transcript_exon_variant	7/8	1
METTL2B	ENST00000480046.5 linkuse as main transcript	c.747T>C	p.Tyr249Tyr	synonymous_variant	7/8	2		ENSP00000418402.1	Q6P1Q9-2
METTL2B	ENST00000481392.1 linkuse as main transcript	c.234T>C	p.Tyr78Tyr	synonymous_variant	3/5	3		ENSP00000418989.1	H7C552

Frequencies

GnomAD3 genomes

AF:

0.389

AC:

59089

AN:

151886

Hom.:

11567

Cov.:

show subpopulations

Gnomad AFR

AF:

0.408

Gnomad AMI

AF:

0.516

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.379

Gnomad EAS

AF:

0.312

Gnomad SAS

AF:

0.376

Gnomad FIN

AF:

0.361

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.403

Gnomad OTH

AF:

0.375

GnomAD3 exomes

AF:

0.366

AC:

92000

AN:

251384

Hom.:

17240

AF XY:

0.373

AC XY:

50681

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.400

Gnomad AMR exome

AF:

0.253

Gnomad ASJ exome

AF:

0.382

Gnomad EAS exome

AF:

0.304

Gnomad SAS exome

AF:

0.381

Gnomad FIN exome

AF:

0.351

Gnomad NFE exome

AF:

0.401

Gnomad OTH exome

AF:

0.390

GnomAD4 exome

AF:

0.397

AC:

579215

AN:

1460720

Hom.:

116296

Cov.:

AF XY:

0.397

AC XY:

288503

AN XY:

726728

show subpopulations

Gnomad4 AFR exome

AF:

0.406

Gnomad4 AMR exome

AF:

0.258

Gnomad4 ASJ exome

AF:

0.382

Gnomad4 EAS exome

AF:

0.299

Gnomad4 SAS exome

AF:

0.377

Gnomad4 FIN exome

AF:

0.357

Gnomad4 NFE exome

AF:

0.409

Gnomad4 OTH exome

AF:

0.393

GnomAD4 genome

AF:

0.389

AC:

59102

AN:

152004

Hom.:

11566

Cov.:

AF XY:

0.386

AC XY:

28684

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.407

Gnomad4 AMR

AF:

0.319

Gnomad4 ASJ

AF:

0.379

Gnomad4 EAS

AF:

0.311

Gnomad4 SAS

AF:

0.377

Gnomad4 FIN

AF:

0.361

Gnomad4 NFE

AF:

0.403

Gnomad4 OTH

AF:

0.370

Alfa

AF:

0.398

Hom.:

5206

Bravo

AF:

0.387

Asia WGS

AF:

0.310

AC:

1080

AN:

3478

EpiCase

AF:

0.418

EpiControl

AF:

0.412

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

1.5

DANN

Benign

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over