dbSNP rs2275426: MAST2:c.1291-70G>A (chr1-46021880-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_015112.3(MAST2):c.1291-70G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 1,536,424 control chromosomes in the GnomAD database, including 153,473 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 0.45 ( 15198 hom., cov: 32)

Exomes 𝑓: 0.44 ( 138275 hom. )

Consequence

MAST2
NM_015112.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.731

Publications

24 publications found

Variant links:

Genes affected

MAST2 (HGNC:19035): (microtubule associated serine/threonine kinase 2) Enables phosphatase binding activity. Predicted to be involved in several processes, including peptidyl-serine phosphorylation; regulation of interleukin-12 production; and spermatid differentiation. Predicted to be located in cytoplasm and plasma membrane. Predicted to be active in microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

MAST2 Gene-Disease associations (from GenCC):

thrombotic disease
Inheritance: AD Classification: LIMITED Submitted by: ClinGen

MAST2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_015112.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015112.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAST2	NM_015112.3	MANE Select	c.1291-70G>A	intron	N/A	NP_055927.2	Q6P0Q8-1
MAST2	NM_001324320.2		c.1312-70G>A	intron	N/A	NP_001311249.1
MAST2	NM_001319245.2		c.1291-70G>A	intron	N/A	NP_001306174.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAST2	ENST00000361297.7	TSL:1 MANE Select	c.1291-70G>A	intron	N/A	ENSP00000354671.2	Q6P0Q8-1
MAST2	ENST00000904602.1		c.1486-70G>A	intron	N/A	ENSP00000574661.1
MAST2	ENST00000904601.1		c.1312-70G>A	intron	N/A	ENSP00000574660.1

Frequencies

GnomAD3 genomes

AF:

0.446

AC:

67601

AN:

151652

Hom.:

15213

Cov.:

show subpopulations

Gnomad AFR

AF:

0.421

Gnomad AMI

AF:

0.466

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.467

Gnomad EAS

AF:

0.628

Gnomad SAS

AF:

0.447

Gnomad FIN

AF:

0.411

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.442

Gnomad OTH

AF:

0.441

GnomAD4 exome

AF:

0.444

AC:

615107

AN:

1384654

Hom.:

138275

AF XY:

0.444

AC XY:

306048

AN XY:

689652

show subpopulations

African (AFR)

AF:

0.412

AC:

13182

AN:

31978

American (AMR)

AF:

0.532

AC:

22811

AN:

42888

Ashkenazi Jewish (ASJ)

AF:

0.462

AC:

11135

AN:

24092

East Asian (EAS)

AF:

0.642

AC:

25138

AN:

39140

South Asian (SAS)

AF:

0.437

AC:

35280

AN:

80794

European-Finnish (FIN)

AF:

0.419

AC:

21876

AN:

52272

Middle Eastern (MID)

AF:

0.406

AC:

2243

AN:

5518

European-Non Finnish (NFE)

AF:

0.436

AC:

457572

AN:

1050398

Other (OTH)

AF:

0.449

AC:

25870

AN:

57574

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

15474

30948

46423

61897

77371

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13862

27724

41586

55448

69310

<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:

0.445

AC:

67581

AN:

151770

Hom.:

15198

Cov.:

AF XY:

0.446

AC XY:

33070

AN XY:

74166

show subpopulations

African (AFR)

AF:

0.420

AC:

17388

AN:

41376

American (AMR)

AF:

0.488

AC:

7443

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.467

AC:

1620

AN:

3468

East Asian (EAS)

AF:

0.627

AC:

3209

AN:

5122

South Asian (SAS)

AF:

0.446

AC:

2145

AN:

4812

European-Finnish (FIN)

AF:

0.411

AC:

4329

AN:

10530

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.442

AC:

29997

AN:

67902

Other (OTH)

AF:

0.435

AC:

917

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1962

3924

5887

7849

9811

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.443

Hom.:

6739

Bravo

AF:

0.451

Asia WGS

AF:

0.522

AC:

1813

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.0030

(source)

DANN

Benign

0.60

PhyloP100

-0.73

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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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