Variant 19-18123631-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001393504.1(MAST3):c.609C>T(p.His203His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 1,585,874 control chromosomes in the GnomAD database, including 228,441 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 0.52 ( 20396 hom., cov: 33)

Exomes 𝑓: 0.54 ( 208045 hom. )

Consequence

MAST3
NM_001393504.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.03

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 links:

MAST3 (HGNC:):

MAST3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP7

Synonymous conserved (PhyloP=-2.03 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAST3	NM_001393504.1 linkuse as main transcript	c.609C>T	p.His203His	synonymous_variant	8/28	ENST00000687212.1	NP_001380433.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAST3	ENST00000687212.1 linkuse as main transcript	c.609C>T	p.His203His	synonymous_variant	8/28		NM_001393504.1	ENSP00000509890.1		A0A8I5KST9

Frequencies

GnomAD3 genomes

AF:

0.516

AC:

78340

AN:

151958

Hom.:

20395

Cov.:

show subpopulations

Gnomad AFR

AF:

0.464

Gnomad AMI

AF:

0.723

Gnomad AMR

AF:

0.505

Gnomad ASJ

AF:

0.496

Gnomad EAS

AF:

0.675

Gnomad SAS

AF:

0.649

Gnomad FIN

AF:

0.499

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.529

Gnomad OTH

AF:

0.498

GnomAD3 exomes

AF:

0.525

AC:

114027

AN:

217052

Hom.:

30539

AF XY:

0.528

AC XY:

62233

AN XY:

117782

show subpopulations

Gnomad AFR exome

AF:

0.447

Gnomad AMR exome

AF:

0.497

Gnomad ASJ exome

AF:

0.441

Gnomad EAS exome

AF:

0.670

Gnomad SAS exome

AF:

0.624

Gnomad FIN exome

AF:

0.487

Gnomad NFE exome

AF:

0.511

Gnomad OTH exome

AF:

0.503

GnomAD4 exome

AF:

0.537

AC:

769492

AN:

1433798

Hom.:

208045

Cov.:

AF XY:

0.538

AC XY:

382745

AN XY:

710964

show subpopulations

Gnomad4 AFR exome

AF:

0.448

Gnomad4 AMR exome

AF:

0.498

Gnomad4 ASJ exome

AF:

0.467

Gnomad4 EAS exome

AF:

0.678

Gnomad4 SAS exome

AF:

0.633

Gnomad4 FIN exome

AF:

0.496

Gnomad4 NFE exome

AF:

0.533

Gnomad4 OTH exome

AF:

0.528

GnomAD4 genome

AF:

0.515

AC:

78364

AN:

152076

Hom.:

20396

Cov.:

AF XY:

0.514

AC XY:

38211

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.464

Gnomad4 AMR

AF:

0.505

Gnomad4 ASJ

AF:

0.496

Gnomad4 EAS

AF:

0.675

Gnomad4 SAS

AF:

0.649

Gnomad4 FIN

AF:

0.499

Gnomad4 NFE

AF:

0.529

Gnomad4 OTH

AF:

0.502

Alfa

AF:

0.519

Hom.:

36138

Bravo

AF:

0.510

Asia WGS

AF:

0.625

AC:

2173

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.60

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over