15-41561570-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006293.4(TYRO3):c.340C>T(p.Arg114Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000163 in 1,593,770 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006293.4 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 |
---|---|---|---|---|---|---|---|---|
TYRO3 | NM_006293.4 | c.340C>T | p.Arg114Trp | missense_variant | Exon 3 of 19 | ENST00000263798.8 | NP_006284.2 | |
TYRO3 | NM_001330264.2 | c.205C>T | p.Arg69Trp | missense_variant | Exon 3 of 19 | NP_001317193.1 | ||
TYRO3 | XM_017022543.3 | c.340C>T | p.Arg114Trp | missense_variant | Exon 3 of 19 | XP_016878032.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TYRO3 | ENST00000263798.8 | c.340C>T | p.Arg114Trp | missense_variant | Exon 3 of 19 | 1 | NM_006293.4 | ENSP00000263798.3 | ||
TYRO3 | ENST00000559066.5 | c.205C>T | p.Arg69Trp | missense_variant | Exon 3 of 19 | 5 | ENSP00000454050.1 | |||
TYRO3 | ENST00000560992.1 | n.599C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152232Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000138 AC: 3AN: 217134Hom.: 0 AF XY: 0.00000854 AC XY: 1AN XY: 117070
GnomAD4 exome AF: 0.0000139 AC: 20AN: 1441538Hom.: 0 Cov.: 33 AF XY: 0.0000126 AC XY: 9AN XY: 715142
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152232Hom.: 0 Cov.: 34 AF XY: 0.0000538 AC XY: 4AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.340C>T (p.R114W) alteration is located in exon 3 (coding exon 3) of the TYRO3 gene. This alteration results from a C to T substitution at nucleotide position 340, causing the arginine (R) at amino acid position 114 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at