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15-87880232-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001012338.3(NTRK3):​c.2334+38G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 1,612,112 control chromosomes in the GnomAD database, including 280,717 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.49 ( 20165 hom., cov: 31)
Exomes 𝑓: 0.59 ( 260552 hom. )

Consequence

NTRK3
NM_001012338.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.297
Variant links:
Genes affected
NTRK3 (HGNC:8033): (neurotrophic receptor tyrosine kinase 3) This gene encodes a member of the neurotrophic tyrosine receptor kinase (NTRK) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. Signalling through this kinase leads to cell differentiation and may play a role in the development of proprioceptive neurons that sense body position. Mutations in this gene have been associated with medulloblastomas, secretory breast carcinomas and other cancers. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 15-87880232-C-T is Benign according to our data. Variant chr15-87880232-C-T is described in ClinVar as [Benign]. Clinvar id is 1249082.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NTRK3NM_001012338.3 linkuse as main transcriptc.2334+38G>A intron_variant ENST00000629765.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NTRK3ENST00000629765.3 linkuse as main transcriptc.2334+38G>A intron_variant 1 NM_001012338.3 Q16288-1

Frequencies

GnomAD3 genomes
AF:
0.487
AC:
73877
AN:
151646
Hom.:
20158
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.219
Gnomad AMI
AF:
0.496
Gnomad AMR
AF:
0.546
Gnomad ASJ
AF:
0.609
Gnomad EAS
AF:
0.602
Gnomad SAS
AF:
0.421
Gnomad FIN
AF:
0.589
Gnomad MID
AF:
0.465
Gnomad NFE
AF:
0.610
Gnomad OTH
AF:
0.511
GnomAD3 exomes
AF:
0.547
AC:
137465
AN:
251166
Hom.:
39261
AF XY:
0.548
AC XY:
74454
AN XY:
135766
show subpopulations
Gnomad AFR exome
AF:
0.207
Gnomad AMR exome
AF:
0.544
Gnomad ASJ exome
AF:
0.602
Gnomad EAS exome
AF:
0.598
Gnomad SAS exome
AF:
0.421
Gnomad FIN exome
AF:
0.576
Gnomad NFE exome
AF:
0.611
Gnomad OTH exome
AF:
0.574
GnomAD4 exome
AF:
0.591
AC:
863300
AN:
1460348
Hom.:
260552
Cov.:
35
AF XY:
0.587
AC XY:
426416
AN XY:
726540
show subpopulations
Gnomad4 AFR exome
AF:
0.200
Gnomad4 AMR exome
AF:
0.546
Gnomad4 ASJ exome
AF:
0.604
Gnomad4 EAS exome
AF:
0.622
Gnomad4 SAS exome
AF:
0.416
Gnomad4 FIN exome
AF:
0.581
Gnomad4 NFE exome
AF:
0.619
Gnomad4 OTH exome
AF:
0.570
GnomAD4 genome
AF:
0.487
AC:
73890
AN:
151764
Hom.:
20165
Cov.:
31
AF XY:
0.486
AC XY:
36016
AN XY:
74166
show subpopulations
Gnomad4 AFR
AF:
0.219
Gnomad4 AMR
AF:
0.547
Gnomad4 ASJ
AF:
0.609
Gnomad4 EAS
AF:
0.602
Gnomad4 SAS
AF:
0.420
Gnomad4 FIN
AF:
0.589
Gnomad4 NFE
AF:
0.610
Gnomad4 OTH
AF:
0.507
Alfa
AF:
0.589
Hom.:
45783
Bravo
AF:
0.477
Asia WGS
AF:
0.483
AC:
1684
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 testingGeneDxJun 19, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
6.7
DANN
Benign
0.44

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: rs1560975; hg19: chr15-88423463; COSMIC: COSV62295880; API