Variant chr3-49887514-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_002447.4(MST1R):c.3996C>T(p.Pro1332=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00727 in 1,614,174 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0044 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0076 ( 69 hom. )

Consequence

MST1R
NM_002447.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0270

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 3-49887514-G-A is Benign according to our data. Variant chr3-49887514-G-A is described in ClinVar as [Benign]. Clinvar id is 708319.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.027 with no splicing effect.

BS2

High AC in GnomAd4 at 672 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MST1R	NM_002447.4 linkuse as main transcript	c.3996C>T	p.Pro1332=	synonymous_variant	20/20	ENST00000296474.8	NP_002438.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MST1R	ENST00000296474.8 linkuse as main transcript	c.3996C>T	p.Pro1332=	synonymous_variant	20/20	1	NM_002447.4	ENSP00000296474	P2	Q04912-1
MST1R	ENST00000621387.4 linkuse as main transcript	c.3678C>T	p.Pro1226=	synonymous_variant	18/18	1		ENSP00000482642		Q04912-7
MST1R	ENST00000344206.8 linkuse as main transcript	c.3849C>T	p.Pro1283=	synonymous_variant	19/19	5		ENSP00000341325	A2	Q04912-2
MST1R	ENST00000411578.6 linkuse as main transcript	c.*818C>T		3_prime_UTR_variant, NMD_transcript_variant	19/19	5		ENSP00000407926

Frequencies

GnomAD3 genomes

AF:

0.00441

AC:

672

AN:

152224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00174

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.00314

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00754

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00372

AC:

935

AN:

251124

Hom.:

AF XY:

0.00359

AC XY:

487

AN XY:

135788

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.00226

Gnomad ASJ exome

AF:

0.00129

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000980

Gnomad FIN exome

AF:

0.000370

Gnomad NFE exome

AF:

0.00708

Gnomad OTH exome

AF:

0.00277

GnomAD4 exome

AF:

0.00756

AC:

11058

AN:

1461832

Hom.:

Cov.:

AF XY:

0.00718

AC XY:

5225

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.00117

Gnomad4 AMR exome

AF:

0.00217

Gnomad4 ASJ exome

AF:

0.00157

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000128

Gnomad4 FIN exome

AF:

0.000524

Gnomad4 NFE exome

AF:

0.00944

Gnomad4 OTH exome

AF:

0.00571

GnomAD4 genome

AF:

0.00441

AC:

672

AN:

152342

Hom.:

Cov.:

AF XY:

0.00401

AC XY:

299

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.00173

Gnomad4 AMR

AF:

0.00314

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00113

Gnomad4 NFE

AF:

0.00754

Gnomad4 OTH

AF:

0.00425

Alfa

AF:

0.00512

Hom.:

Bravo

AF:

0.00408

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

1.2

DANN

Benign

0.31

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