Genetic Variant MST1R:c.3811-10C>A (chr3-49890070-G-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_002447.4(MST1R):c.3811-10C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 1,589,556 control chromosomes in the GnomAD database, including 4,798 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.074 ( 444 hom., cov: 32)

Exomes 𝑓: 0.076 ( 4354 hom. )

Consequence

MST1R
NM_002447.4 intron

Scores

Splicing: ADA: 0.003578

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0650

Variant links:

Genes affected

MST1R (HGNC:7381): (macrophage stimulating 1 receptor) This gene encodes a cell surface receptor for macrophage-stimulating protein (MSP) with tyrosine kinase activity. The mature form of this protein is a heterodimer of disulfide-linked alpha and beta subunits, generated by proteolytic cleavage of a single-chain precursor. The beta subunit undergoes tyrosine phosphorylation upon stimulation by MSP. This protein is expressed on the ciliated epithelia of the mucociliary transport apparatus of the lung, and together with MSP, thought to be involved in host defense. Alternative splicing generates multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Jan 2016]

MST1R 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=-0.8).

BP6

Variant 3-49890070-G-T is Benign according to our data. Variant chr3-49890070-G-T is described in ClinVar as [Benign]. Clinvar id is 3055583.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MST1R	NM_002447.4 link	c.3811-10C>A		intron_variant	Intron 18 of 19	ENST00000296474.8	NP_002438.2	Q04912-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MST1R	ENST00000296474.8 link	c.3811-10C>A		intron_variant	Intron 18 of 19	1	NM_002447.4	ENSP00000296474.3		Q04912-1

Frequencies

GnomAD3 genomes

AF:

0.0741

AC:

11279

AN:

152154

Hom.:

444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0888

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.0473

Gnomad ASJ

AF:

0.0709

Gnomad EAS

AF:

0.0250

Gnomad SAS

AF:

0.0565

Gnomad FIN

AF:

0.0673

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0770

Gnomad OTH

AF:

0.0766

GnomAD3 exomes

AF:

0.0625

AC:

14276

AN:

228480

Hom.:

489

AF XY:

0.0629

AC XY:

7693

AN XY:

122380

show subpopulations

Gnomad AFR exome

AF:

0.0906

Gnomad AMR exome

AF:

0.0330

Gnomad ASJ exome

AF:

0.0674

Gnomad EAS exome

AF:

0.0280

Gnomad SAS exome

AF:

0.0557

Gnomad FIN exome

AF:

0.0694

Gnomad NFE exome

AF:

0.0730

Gnomad OTH exome

AF:

0.0660

GnomAD4 exome

AF:

0.0756

AC:

108701

AN:

1437284

Hom.:

4354

Cov.:

AF XY:

0.0747

AC XY:

53208

AN XY:

712376

show subpopulations

Gnomad4 AFR exome

AF:

0.0863

Gnomad4 AMR exome

AF:

0.0350

Gnomad4 ASJ exome

AF:

0.0710

Gnomad4 EAS exome

AF:

0.0210

Gnomad4 SAS exome

AF:

0.0575

Gnomad4 FIN exome

AF:

0.0679

Gnomad4 NFE exome

AF:

0.0812

Gnomad4 OTH exome

AF:

0.0689

GnomAD4 genome

AF:

0.0741

AC:

11285

AN:

152272

Hom.:

444

Cov.:

AF XY:

0.0718

AC XY:

5350

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0887

Gnomad4 AMR

AF:

0.0472

Gnomad4 ASJ

AF:

0.0709

Gnomad4 EAS

AF:

0.0245

Gnomad4 SAS

AF:

0.0570

Gnomad4 FIN

AF:

0.0673

Gnomad4 NFE

AF:

0.0770

Gnomad4 OTH

AF:

0.0777

Alfa

AF:

0.0664

Hom.:

419

Bravo

AF:

0.0737

Asia WGS

AF:

0.0540

AC:

188

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MST1R-related disorder

Benign:1

Dec 16, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.2

DANN

Benign

0.75

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0036

dbscSNV1_RF

Benign

0.11

SpliceAI score (max)

0.050

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