Genetic Variant MAST3:c.161+96C>T (chr19-18110837-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001393504.1(MAST3):c.161+96C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 519,152 control chromosomes in the GnomAD database, including 53,807 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 0.48 ( 17669 hom., cov: 32)

Exomes 𝑓: 0.43 ( 36138 hom. )

Consequence

MAST3
NM_001393504.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.276

Publications

8 publications found

Variant links:

Genes affected

MAST3 (HGNC:19036): (microtubule associated serine/threonine kinase 3) Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in cytoskeleton organization; intracellular signal transduction; and peptidyl-serine phosphorylation. [provided by Alliance of Genome Resources, Apr 2022]

MAST3 Gene-Disease associations (from GenCC):

developmental and epileptic encephalopathy 108
Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

MAST3 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393504.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAST3	NM_001393504.1	MANE Select	c.161+96C>T	intron	N/A	NP_001380433.1	A0A8I5KST9
MAST3	NM_001393501.1		c.161+96C>T	intron	N/A	NP_001380430.1
MAST3	NM_001393502.1		c.161+96C>T	intron	N/A	NP_001380431.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAST3	ENST00000687212.1	MANE Select	c.161+96C>T	intron	N/A	ENSP00000509890.1	A0A8I5KST9
MAST3	ENST00000262811.10	TSL:1	c.71+3219C>T	intron	N/A	ENSP00000262811.4	O60307
MAST3	ENST00000697701.1		c.137+96C>T	intron	N/A	ENSP00000513408.1	A0A8V8TLL8

Frequencies

GnomAD3 genomes

AF:

0.476

AC:

72395

AN:

151934

Hom.:

17636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.553

Gnomad AMI

AF:

0.276

Gnomad AMR

AF:

0.483

Gnomad ASJ

AF:

0.461

Gnomad EAS

AF:

0.321

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.503

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.495

GnomAD4 exome

AF:

0.433

AC:

158857

AN:

367098

Hom.:

36138

AF XY:

0.432

AC XY:

74746

AN XY:

173008

show subpopulations

African (AFR)

AF:

0.560

AC:

3662

AN:

6534

American (AMR)

AF:

0.462

AC:

181

AN:

392

Ashkenazi Jewish (ASJ)

AF:

0.470

AC:

1067

AN:

2270

East Asian (EAS)

AF:

0.307

AC:

461

AN:

1504

South Asian (SAS)

AF:

0.255

AC:

1858

AN:

7288

European-Finnish (FIN)

AF:

0.484

AC:

270

AN:

558

Middle Eastern (MID)

AF:

0.463

AC:

334

AN:

722

European-Non Finnish (NFE)

AF:

0.435

AC:

145900

AN:

335722

Other (OTH)

AF:

0.423

AC:

5124

AN:

12108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

4233

8465

12698

16930

21163

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5920

11840

17760

23680

29600

<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:

0.477

AC:

72486

AN:

152054

Hom.:

17669

Cov.:

AF XY:

0.477

AC XY:

35447

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.554

AC:

22953

AN:

41464

American (AMR)

AF:

0.483

AC:

7386

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.461

AC:

1601

AN:

3470

East Asian (EAS)

AF:

0.322

AC:

1660

AN:

5158

South Asian (SAS)

AF:

0.272

AC:

1314

AN:

4826

European-Finnish (FIN)

AF:

0.503

AC:

5321

AN:

10572

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.454

AC:

30826

AN:

67950

Other (OTH)

AF:

0.491

AC:

1039

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1892

3783

5675

7566

9458

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

644

1288

1932

2576

3220

<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:

0.465

Hom.:

42478

Bravo

AF:

0.484

Asia WGS

AF:

0.338

AC:

1179

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.7

(source)

DANN

Benign

0.74

PhyloP100

-0.28

Mutation Taster

=100/0

polymorphism (auto)

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over