rs72481816
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000317501.9(NTRK3):c.*1004C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000586 in 230,516 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00063 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00050 ( 0 hom. )
Consequence
NTRK3
ENST00000317501.9 3_prime_UTR
ENST00000317501.9 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.31
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BS2
?
High AC in GnomAd4 at 96 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NTRK3 | NM_001012338.3 | c.1586-37588C>G | intron_variant | ENST00000629765.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NTRK3 | ENST00000629765.3 | c.1586-37588C>G | intron_variant | 1 | NM_001012338.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000631 AC: 96AN: 152162Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000498 AC: 39AN: 78236Hom.: 0 Cov.: 0 AF XY: 0.000526 AC XY: 19AN XY: 36152
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GnomAD4 genome ? AF: 0.000630 AC: 96AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.000631 AC XY: 47AN XY: 74448
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ClinVar
Not reported inComputational scores
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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