rs28521337
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000317501.9(NTRK3):c.*1296G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 232,960 control chromosomes in the GnomAD database, including 45,227 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 0.63 ( 31291 hom., cov: 33)
Exomes 𝑓: 0.57 ( 13936 hom. )
Consequence
NTRK3
ENST00000317501.9 3_prime_UTR
ENST00000317501.9 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.208
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=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NTRK3 | NM_001012338.3 | c.1586-37296G>C | intron_variant | ENST00000629765.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NTRK3 | ENST00000629765.3 | c.1586-37296G>C | intron_variant | 1 | NM_001012338.3 |
Frequencies
GnomAD3 genomes ? AF: 0.625 AC: 95011AN: 151986Hom.: 31222 Cov.: 33
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GnomAD4 exome AF: 0.575 AC: 46489AN: 80856Hom.: 13936 Cov.: 0 AF XY: 0.572 AC XY: 21392AN XY: 37366
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GnomAD4 genome ? AF: 0.625 AC: 95138AN: 152104Hom.: 31291 Cov.: 33 AF XY: 0.623 AC XY: 46292AN XY: 74328
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at