Variant rs73598041 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001172303.3(MASTL):c.2483-33T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 in 1,592,828 control chromosomes in the GnomAD database, including 2,009 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 257 hom., cov: 33)

Exomes 𝑓: 0.047 ( 1752 hom. )

Consequence

MASTL
NM_001172303.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.14

Variant links:

Genes affected

MASTL (HGNC:19042): (microtubule associated serine/threonine kinase like) This gene encodes a microtubule-associated serine/threonine kinase. Mutations at this locus have been associated with autosomal dominant thrombocytopenia, also known as thrombocytopenia-2. Alternatively spliced transcript variants have been described for this locus. [provided by RefSeq, Feb 2010]

MASTL links:

ACBD5 (HGNC:23338): (acyl-CoA binding domain containing 5) This gene encodes a member of the acyl-Coenzyme A binding protein family, known to function in the transport and distribution of long chain acyl-Coenzyme A in cells. This gene may play a role in the differentiation of megakaryocytes and formation of platelets. A related protein in yeast is involved in autophagy of peroxisomes. A mutation in this gene has been associated with autosomal dominant thrombocytopenia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

ACBD5 links:

MASTL (HGNC:):

MASTL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 10-27186346-T-C is Benign according to our data. Variant chr10-27186346-T-C is described in ClinVar as [Benign]. Clinvar id is 262121.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MASTL	NM_001172303.3 linkuse as main transcript	c.2483-33T>C		intron_variant		ENST00000375940.9	NP_001165774.1	Q96GX5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MASTL	ENST00000375940.9 linkuse as main transcript	c.2483-33T>C		intron_variant		1	NM_001172303.3	ENSP00000365107.5		Q96GX5-1

Frequencies

GnomAD3 genomes

AF:

0.0558

AC:

8490

AN:

152180

Hom.:

255

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0822

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0330

Gnomad ASJ

AF:

0.0674

Gnomad EAS

AF:

0.00307

Gnomad SAS

AF:

0.0323

Gnomad FIN

AF:

0.0519

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0514

Gnomad OTH

AF:

0.0440

GnomAD3 exomes

AF:

0.0439

AC:

11018

AN:

250982

Hom.:

310

AF XY:

0.0435

AC XY:

5906

AN XY:

135736

show subpopulations

Gnomad AFR exome

AF:

0.0832

Gnomad AMR exome

AF:

0.0188

Gnomad ASJ exome

AF:

0.0631

Gnomad EAS exome

AF:

0.00348

Gnomad SAS exome

AF:

0.0346

Gnomad FIN exome

AF:

0.0553

Gnomad NFE exome

AF:

0.0512

Gnomad OTH exome

AF:

0.0415

GnomAD4 exome

AF:

0.0470

AC:

67675

AN:

1440530

Hom.:

1752

Cov.:

AF XY:

0.0467

AC XY:

33539

AN XY:

718024

show subpopulations

Gnomad4 AFR exome

AF:

0.0847

Gnomad4 AMR exome

AF:

0.0198

Gnomad4 ASJ exome

AF:

0.0636

Gnomad4 EAS exome

AF:

0.00195

Gnomad4 SAS exome

AF:

0.0350

Gnomad4 FIN exome

AF:

0.0557

Gnomad4 NFE exome

AF:

0.0487

Gnomad4 OTH exome

AF:

0.0477

GnomAD4 genome

AF:

0.0559

AC:

8511

AN:

152298

Hom.:

257

Cov.:

AF XY:

0.0547

AC XY:

4076

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0825

Gnomad4 AMR

AF:

0.0330

Gnomad4 ASJ

AF:

0.0674

Gnomad4 EAS

AF:

0.00308

Gnomad4 SAS

AF:

0.0321

Gnomad4 FIN

AF:

0.0519

Gnomad4 NFE

AF:

0.0514

Gnomad4 OTH

AF:

0.0435

Alfa

AF:

0.0576

Hom.:

Bravo

AF:

0.0561

Asia WGS

AF:

0.0350

AC:

123

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.3

DANN

Benign

0.46

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over