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GeneBe

rs7180942

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001012338.3(NTRK3):c.1205-2611A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,166 control chromosomes in the GnomAD database, including 24,581 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.55 ( 24581 hom., cov: 34)

Consequence

NTRK3
NM_001012338.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.362
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NTRK3NM_001012338.3 linkuse as main transcriptc.1205-2611A>G intron_variant ENST00000629765.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NTRK3ENST00000629765.3 linkuse as main transcriptc.1205-2611A>G intron_variant 1 NM_001012338.3 Q16288-1

Frequencies

GnomAD3 genomes
AF:
0.550
AC:
83586
AN:
152048
Hom.:
24535
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.778
Gnomad AMI
AF:
0.471
Gnomad AMR
AF:
0.443
Gnomad ASJ
AF:
0.546
Gnomad EAS
AF:
0.370
Gnomad SAS
AF:
0.472
Gnomad FIN
AF:
0.393
Gnomad MID
AF:
0.544
Gnomad NFE
AF:
0.480
Gnomad OTH
AF:
0.519
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.550
AC:
83697
AN:
152166
Hom.:
24581
Cov.:
34
AF XY:
0.541
AC XY:
40264
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.778
Gnomad4 AMR
AF:
0.443
Gnomad4 ASJ
AF:
0.546
Gnomad4 EAS
AF:
0.370
Gnomad4 SAS
AF:
0.473
Gnomad4 FIN
AF:
0.393
Gnomad4 NFE
AF:
0.480
Gnomad4 OTH
AF:
0.523
Alfa
AF:
0.517
Hom.:
2635
Bravo
AF:
0.560
Asia WGS
AF:
0.458
AC:
1595
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
5.8
Dann
Benign
0.28

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs7180942; hg19: chr15-88674576; API