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GeneBe

3-49887514-G-A

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

2

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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.027 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 672 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MST1RNM_002447.4 linkuse as main transcriptc.3996C>T p.Pro1332= synonymous_variant 20/20 ENST00000296474.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MST1RENST00000296474.8 linkuse as main transcriptc.3996C>T p.Pro1332= synonymous_variant 20/201 NM_002447.4 P2Q04912-1
MST1RENST00000621387.4 linkuse as main transcriptc.3678C>T p.Pro1226= synonymous_variant 18/181 Q04912-7
MST1RENST00000344206.8 linkuse as main transcriptc.3849C>T p.Pro1283= synonymous_variant 19/195 A2Q04912-2
MST1RENST00000411578.6 linkuse as main transcriptc.*818C>T 3_prime_UTR_variant, NMD_transcript_variant 19/195

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00441
AC:
672
AN:
152224
Hom.:
0
Cov.:
33
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.:
4
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.:
69
Cov.:
34
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00441
AC:
672
AN:
152342
Hom.:
0
Cov.:
33
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.:
2
Bravo
AF:
0.00408
Asia WGS
AF:
0.000577
AC:
2
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 submitterclinical testingInvitaeDec 31, 2019- -

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.

Other links and lift over

dbSNP: rs5030975; hg19: chr3-49924947; COSMIC: COSV56574273; COSMIC: COSV56574273; API