Genetic Variant MAT2B:c.63+67T>G (chr5-163505816-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013283.5(MAT2B):c.63+67T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,208,942 control chromosomes in the GnomAD database, including 15,327 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 0.17 ( 2263 hom., cov: 31)

Exomes 𝑓: 0.16 ( 13064 hom. )

Consequence

MAT2B
NM_013283.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.28

Publications

1 publications found

Variant links:

Genes affected

MAT2B (HGNC:6905): (methionine adenosyltransferase 2 non-catalytic beta subunit) The protein encoded by this gene belongs to the methionine adenosyltransferase (MAT) family. MAT catalyzes the biosynthesis of S-adenosylmethionine from methionine and ATP. This protein is the regulatory beta subunit of MAT. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2012]

MAT2B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013283.5. 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
	MAT2B	NM_013283.5	MANE Select	c.63+67T>G		intron	N/A	NP_037415.1	A0A140VJP2
	MAT2B	NM_182796.2		c.30+2392T>G		intron	N/A	NP_877725.1	Q9NZL9-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAT2B	ENST00000321757.11	TSL:1 MANE Select	c.63+67T>G	intron	N/A	ENSP00000325425.6	Q9NZL9-1
MAT2B	ENST00000280969.9	TSL:1	c.30+2392T>G	intron	N/A	ENSP00000280969.5	Q9NZL9-2
MAT2B	ENST00000518095.5	TSL:1	c.63+67T>G	intron	N/A	ENSP00000428046.1	Q9NZL9-3

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25381

AN:

151886

Hom.:

2262

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.0697

Gnomad SAS

AF:

0.132

Gnomad FIN

AF:

0.229

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.158

GnomAD4 exome

AF:

0.156

AC:

164793

AN:

1056938

Hom.:

13064

AF XY:

0.156

AC XY:

78229

AN XY:

500162

show subpopulations

African (AFR)

AF:

0.193

AC:

4287

AN:

22206

American (AMR)

AF:

0.123

AC:

1028

AN:

8388

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

2171

AN:

14124

East Asian (EAS)

AF:

0.102

AC:

2699

AN:

26362

South Asian (SAS)

AF:

0.133

AC:

2503

AN:

18806

European-Finnish (FIN)

AF:

0.229

AC:

8356

AN:

36490

Middle Eastern (MID)

AF:

0.204

AC:

608

AN:

2978

European-Non Finnish (NFE)

AF:

0.155

AC:

136759

AN:

885072

Other (OTH)

AF:

0.150

AC:

6382

AN:

42512

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

6922

13844

20765

27687

34609

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5532

11064

16596

22128

27660

<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:

0.167

AC:

25402

AN:

152004

Hom.:

2263

Cov.:

AF XY:

0.168

AC XY:

12496

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.185

AC:

7655

AN:

41464

American (AMR)

AF:

0.131

AC:

1995

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.153

AC:

530

AN:

3466

East Asian (EAS)

AF:

0.0701

AC:

361

AN:

5152

South Asian (SAS)

AF:

0.132

AC:

637

AN:

4812

European-Finnish (FIN)

AF:

0.229

AC:

2423

AN:

10570

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.164

AC:

11167

AN:

67946

Other (OTH)

AF:

0.162

AC:

341

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1073

2147

3220

4294

5367

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

278

556

834

1112

1390

<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:

0.175

Hom.:

310

Bravo

AF:

0.163

Asia WGS

AF:

0.150

AC:

522

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.33

(source)

DANN

Benign

0.36

PhyloP100

-2.3

PromoterAI

-0.031

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over