10-62199807-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_145307.4(RTKN2):c.1241G>A(p.Arg414Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000806 in 1,613,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145307.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RTKN2 | ENST00000373789.8 | c.1241G>A | p.Arg414Gln | missense_variant | Exon 11 of 12 | 1 | NM_145307.4 | ENSP00000362894.3 | ||
RTKN2 | ENST00000315289.6 | c.647G>A | p.Arg216Gln | missense_variant | Exon 7 of 9 | 2 | ENSP00000325379.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152060Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251302Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135820
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461386Hom.: 0 Cov.: 29 AF XY: 0.00000550 AC XY: 4AN XY: 727012
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152060Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1241G>A (p.R414Q) alteration is located in exon 11 (coding exon 11) of the RTKN2 gene. This alteration results from a G to A substitution at nucleotide position 1241, causing the arginine (R) at amino acid position 414 to be replaced by a glutamine (Q). 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