Genetic Variant MAT2A:c.952-49A>G (chr2-85542852-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005911.6(MAT2A):c.952-49A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 1,593,930 control chromosomes in the GnomAD database, including 62,648 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 6965 hom., cov: 32)

Exomes 𝑓: 0.27 ( 55683 hom. )

Consequence

MAT2A
NM_005911.6 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.987

Variant links:

Genes affected

MAT2A (HGNC:6904): (methionine adenosyltransferase 2A) The protein encoded by this gene catalyzes the production of S-adenosylmethionine (AdoMet) from methionine and ATP. AdoMet is the key methyl donor in cellular processes. [provided by RefSeq, Jun 2011]

MAT2A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 2-85542852-A-G is Benign according to our data. Variant chr2-85542852-A-G is described in ClinVar as [Benign]. Clinvar id is 674849.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAT2A	NM_005911.6 link	c.952-49A>G		intron_variant	Intron 7 of 8	ENST00000306434.8	NP_005902.1	P31153-1A0A140VJP5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MAT2A	ENST00000306434.8 link	c.952-49A>G	intron_variant	Intron 7 of 8	1	NM_005911.6	ENSP00000303147.3	P31153-1
MAT2A	ENST00000409017.1 link	c.763-49A>G	intron_variant	Intron 7 of 7	1		ENSP00000386353.1	P31153-2
MAT2A	ENST00000481412.5 link	n.1121-49A>G	intron_variant	Intron 6 of 6	1

Frequencies

GnomAD3 genomes

AF:

0.297

AC:

45181

AN:

151960

Hom.:

6953

Cov.:

show subpopulations

Gnomad AFR

AF:

0.364

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.225

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.324

Gnomad SAS

AF:

0.168

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.278

GnomAD3 exomes

AF:

0.264

AC:

63065

AN:

239198

Hom.:

8771

AF XY:

0.261

AC XY:

33843

AN XY:

129488

show subpopulations

Gnomad AFR exome

AF:

0.370

Gnomad AMR exome

AF:

0.190

Gnomad ASJ exome

AF:

0.233

Gnomad EAS exome

AF:

0.321

Gnomad SAS exome

AF:

0.163

Gnomad FIN exome

AF:

0.310

Gnomad NFE exome

AF:

0.282

Gnomad OTH exome

AF:

0.257

GnomAD4 exome

AF:

0.275

AC:

396458

AN:

1441852

Hom.:

55683

Cov.:

AF XY:

0.272

AC XY:

194922

AN XY:

716546

show subpopulations

Gnomad4 AFR exome

AF:

0.360

Gnomad4 AMR exome

AF:

0.197

Gnomad4 ASJ exome

AF:

0.236

Gnomad4 EAS exome

AF:

0.313

Gnomad4 SAS exome

AF:

0.168

Gnomad4 FIN exome

AF:

0.301

Gnomad4 NFE exome

AF:

0.282

Gnomad4 OTH exome

AF:

0.274

GnomAD4 genome

AF:

0.297

AC:

45218

AN:

152078

Hom.:

6965

Cov.:

AF XY:

0.295

AC XY:

21928

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.364

Gnomad4 AMR

AF:

0.224

Gnomad4 ASJ

AF:

0.218

Gnomad4 EAS

AF:

0.324

Gnomad4 SAS

AF:

0.168

Gnomad4 FIN

AF:

0.321

Gnomad4 NFE

AF:

0.281

Gnomad4 OTH

AF:

0.283

Alfa

AF:

0.266

Hom.:

6573

Bravo

AF:

0.297

Asia WGS

AF:

0.278

AC:

966

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 18, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.26

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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