Variant rs12572707 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.465-32G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 1,368,716 control chromosomes in the GnomAD database, including 4,308 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.075 ( 497 hom., cov: 31)

Exomes 𝑓: 0.067 ( 3811 hom. )

Consequence

MASTL
NM_001172303.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0140

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=-0.83).

BP6

Variant 10-27161062-G-C is Benign according to our data. Variant chr10-27161062-G-C is described in ClinVar as [Benign]. Clinvar id is 262124.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.151 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.465-32G>C		intron_variant		ENST00000375940.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
MASTL	ENST00000375940.9 linkuse as main transcript	c.465-32G>C	intron_variant	1	NM_001172303.3	P5	Q96GX5-1
MASTL	ENST00000375946.8 linkuse as main transcript	c.465-32G>C	intron_variant	1		A1	Q96GX5-3
MASTL	ENST00000342386.10 linkuse as main transcript	c.465-32G>C	intron_variant	2			Q96GX5-2

Frequencies

GnomAD3 genomes

AF:

0.0753

AC:

11415

AN:

151562

Hom.:

495

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0924

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0516

Gnomad ASJ

AF:

0.0772

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0543

Gnomad OTH

AF:

0.0542

GnomAD3 exomes

AF:

0.0835

AC:

20742

AN:

248298

Hom.:

1087

AF XY:

0.0853

AC XY:

11455

AN XY:

134314

show subpopulations

Gnomad AFR exome

AF:

0.0926

Gnomad AMR exome

AF:

0.0673

Gnomad ASJ exome

AF:

0.0733

Gnomad EAS exome

AF:

0.151

Gnomad SAS exome

AF:

0.148

Gnomad FIN exome

AF:

0.113

Gnomad NFE exome

AF:

0.0553

Gnomad OTH exome

AF:

0.0687

GnomAD4 exome

AF:

0.0674

AC:

81972

AN:

1217036

Hom.:

3811

Cov.:

AF XY:

0.0697

AC XY:

43081

AN XY:

617688

show subpopulations

Gnomad4 AFR exome

AF:

0.0952

Gnomad4 AMR exome

AF:

0.0647

Gnomad4 ASJ exome

AF:

0.0742

Gnomad4 EAS exome

AF:

0.207

Gnomad4 SAS exome

AF:

0.144

Gnomad4 FIN exome

AF:

0.109

Gnomad4 NFE exome

AF:

0.0510

Gnomad4 OTH exome

AF:

0.0680

GnomAD4 genome

AF:

0.0754

AC:

11437

AN:

151680

Hom.:

497

Cov.:

AF XY:

0.0795

AC XY:

5893

AN XY:

74114

show subpopulations

Gnomad4 AFR

AF:

0.0929

Gnomad4 AMR

AF:

0.0515

Gnomad4 ASJ

AF:

0.0772

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.156

Gnomad4 FIN

AF:

0.109

Gnomad4 NFE

AF:

0.0543

Gnomad4 OTH

AF:

0.0541

Alfa

AF:

0.0423

Hom.:

Bravo

AF:

0.0713

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.4

DANN

Benign

0.58

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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