rs200698390
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006180.6(NTRK2):c.56G>A(p.Cys19Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000657 in 152,244 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_006180.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTRK2 | NM_006180.6 | c.56G>A | p.Cys19Tyr | missense_variant | Exon 2 of 19 | ENST00000277120.8 | NP_006171.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 33
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74388
ClinVar
Submissions by phenotype
NTRK2-related disorder Uncertain:1
The NTRK2 c.56G>A variant is predicted to result in the amino acid substitution p.Cys19Tyr. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Developmental and epileptic encephalopathy, 58 Uncertain:1
The variant NM_006180.6:c.56G>A results in the substitution of cysteine with tyrosine at position 19 in the protein. Cysteine is a sulfur-containing amino acid, while tyrosine is aromatic and polar, which could potentially affect the protein's structure or function, particularly if the cysteine residue is involved in disulfide bonding. Based on PP2 (observed in a gene with a known functional effect) and PM2 (absence from controls or databases), this variant is classified as of uncertain significance (VUS). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at