chr2-85541207-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005911.6(MAT2A):c.169+47A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00297 in 1,612,154 control chromosomes in the GnomAD database, including 118 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.016 ( 66 hom., cov: 33)

Exomes 𝑓: 0.0016 ( 52 hom. )

Consequence

MAT2A
NM_005911.6 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.303

Publications

4 publications found

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 Gene-Disease associations (from GenCC):

familial thoracic aortic aneurysm and aortic dissection
Inheritance: AD Classification: LIMITED Submitted by: ClinGen

MAT2A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 2-85541207-A-G is Benign according to our data. Variant chr2-85541207-A-G is described in CliVar as Benign. Clinvar id is 679091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-85541207-A-G is described in CliVar as Benign. Clinvar id is 679091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-85541207-A-G is described in CliVar as Benign. Clinvar id is 679091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-85541207-A-G is described in CliVar as Benign. Clinvar id is 679091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-85541207-A-G is described in CliVar as Benign. Clinvar id is 679091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-85541207-A-G is described in CliVar as Benign. Clinvar id is 679091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-85541207-A-G is described in CliVar as Benign. Clinvar id is 679091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-85541207-A-G is described in CliVar as Benign. Clinvar id is 679091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-85541207-A-G is described in CliVar as Benign. Clinvar id is 679091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAT2A	NM_005911.6 link	c.169+47A>G		intron_variant	Intron 2 of 8	ENST00000306434.8	NP_005902.1	P31153-1A0A140VJP5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAT2A	ENST00000306434.8 link	c.169+47A>G		intron_variant	Intron 2 of 8	1	NM_005911.6	ENSP00000303147.3		P31153-1

Frequencies

GnomAD3 genomes

AF:

0.0158

AC:

2412

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0545

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00733

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000250

Gnomad OTH

AF:

0.00813

GnomAD2 exomes

AF:

0.00426

AC:

1065

AN:

250210

AF XY:

0.00311

show subpopulations

Gnomad AFR exome

AF:

0.0546

Gnomad AMR exome

AF:

0.00365

Gnomad ASJ exome

AF:

0.00120

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000221

Gnomad OTH exome

AF:

0.00312

GnomAD4 exome

AF:

0.00163

AC:

2380

AN:

1459848

Hom.:

Cov.:

AF XY:

0.00142

AC XY:

1030

AN XY:

726100

show subpopulations

African (AFR)

AF:

0.0528

AC:

1760

AN:

33356

American (AMR)

AF:

0.00400

AC:

178

AN:

44484

Ashkenazi Jewish (ASJ)

AF:

0.00172

AC:

AN:

26102

East Asian (EAS)

AF:

0.00

AC:

AN:

39660

South Asian (SAS)

AF:

0.0000582

AC:

AN:

85954

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53412

Middle Eastern (MID)

AF:

0.00417

AC:

AN:

5758

European-Non Finnish (NFE)

AF:

0.000140

AC:

156

AN:

1110834

Other (OTH)

AF:

0.00352

AC:

212

AN:

60288

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

130

261

391

522

652

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

180

240

300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0158

AC:

2413

AN:

152306

Hom.:

Cov.:

AF XY:

0.0154

AC XY:

1144

AN XY:

74486

show subpopulations

African (AFR)

AF:

0.0544

AC:

2259

AN:

41558

American (AMR)

AF:

0.00732

AC:

112

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00115

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5192

South Asian (SAS)

AF:

0.000207

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0000942

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000250

AC:

AN:

68028

Other (OTH)

AF:

0.00804

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

110

220

330

440

550

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00734

Hom.:

Bravo

AF:

0.0182

Asia WGS

AF:

0.00260

AC:

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

Jun 14, 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. -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.73

(source)

DANN

Benign

0.71

PhyloP100

-0.30

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over