rs3784415

chr15-88110250-A-Cchr15-88110250-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001012338.3(NTRK3):c.1396+16021T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,186 control chromosomes in the GnomAD database, including 2,480 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 0.15 (2480 hom., cov: 33)
• Consequence: NTRK3 NM_001012338.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTRK3	NM_001012338.3	c.1396+16021T>G		intron_variant		ENST00000629765.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTRK3	ENST00000629765.3	c.1396+16021T>G		intron_variant		1	NM_001012338.3

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23252 AN: 152068 Hom.: 2475 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.0432

Gnomad SAS AF: 0.0307

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.147

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.153 AC: 23276 AN: 152186 Hom.: 2480 Cov.: 33 AF XY: 0.147 AC XY: 10963 AN XY: 74408

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0975

Gnomad4 EAS AF: 0.0435

Gnomad4 SAS AF: 0.0313

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.146

Alfa AF: 0.110 Hom.: 1343

Bravo AF: 0.166

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.3
Dann	Benign	0.69

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

Other links and lift over

dbSNP: rs3784415; hg19: chr15-88653481;