Variant chr10-27155649-C-T 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.186+37C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0479 in 1,610,346 control chromosomes in the GnomAD database, including 2,032 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 258 hom., cov: 33)

Exomes 𝑓: 0.047 ( 1774 hom. )

Consequence

MASTL
NM_001172303.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.532

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 10-27155649-C-T is Benign according to our data. Variant chr10-27155649-C-T is described in ClinVar as [Benign]. Clinvar id is 262117.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	UniProt
MASTL	NM_001172303.3 linkuse as main transcript	c.186+37C>T		intron_variant		ENST00000375940.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
MASTL	ENST00000375940.9 linkuse as main transcript	c.186+37C>T	intron_variant	1	NM_001172303.3	P5	Q96GX5-1
MASTL	ENST00000375946.8 linkuse as main transcript	c.186+37C>T	intron_variant	1		A1	Q96GX5-3
MASTL	ENST00000342386.10 linkuse as main transcript	c.186+37C>T	intron_variant	2			Q96GX5-2

Frequencies

GnomAD3 genomes

AF:

0.0558

AC:

8493

AN:

152170

Hom.:

256

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0821

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0331

Gnomad ASJ

AF:

0.0674

Gnomad EAS

AF:

0.00309

Gnomad SAS

AF:

0.0327

Gnomad FIN

AF:

0.0520

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0514

Gnomad OTH

AF:

0.0444

GnomAD3 exomes

AF:

0.0438

AC:

10819

AN:

246740

Hom.:

302

AF XY:

0.0435

AC XY:

5821

AN XY:

133814

show subpopulations

Gnomad AFR exome

AF:

0.0833

Gnomad AMR exome

AF:

0.0188

Gnomad ASJ exome

AF:

0.0633

Gnomad EAS exome

AF:

0.00344

Gnomad SAS exome

AF:

0.0344

Gnomad FIN exome

AF:

0.0556

Gnomad NFE exome

AF:

0.0513

Gnomad OTH exome

AF:

0.0418

GnomAD4 exome

AF:

0.0471

AC:

68670

AN:

1458060

Hom.:

1774

Cov.:

AF XY:

0.0468

AC XY:

33959

AN XY:

725436

show subpopulations

Gnomad4 AFR exome

AF:

0.0851

Gnomad4 AMR exome

AF:

0.0198

Gnomad4 ASJ exome

AF:

0.0636

Gnomad4 EAS exome

AF:

0.00199

Gnomad4 SAS exome

AF:

0.0349

Gnomad4 FIN exome

AF:

0.0557

Gnomad4 NFE exome

AF:

0.0488

Gnomad4 OTH exome

AF:

0.0480

GnomAD4 genome

AF:

0.0559

AC:

8514

AN:

152286

Hom.:

258

Cov.:

AF XY:

0.0548

AC XY:

4079

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.0825

Gnomad4 AMR

AF:

0.0331

Gnomad4 ASJ

AF:

0.0674

Gnomad4 EAS

AF:

0.00310

Gnomad4 SAS

AF:

0.0325

Gnomad4 FIN

AF:

0.0520

Gnomad4 NFE

AF:

0.0514

Gnomad4 OTH

AF:

0.0440

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

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

-0.81

CADD

Benign

8.9

DANN

Benign

0.83

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