2-74428372-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001015055.2(RTKN):āc.982G>Cā(p.Ala328Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001015055.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTKN | NM_001015055.2 | c.982G>C | p.Ala328Pro | missense_variant | 9/12 | ENST00000272430.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTKN | ENST00000272430.10 | c.982G>C | p.Ala328Pro | missense_variant | 9/12 | 1 | NM_001015055.2 | P4 | |
RTKN | ENST00000233330.6 | c.832G>C | p.Ala278Pro | missense_variant | 9/12 | 1 | |||
RTKN | ENST00000305557.9 | c.943G>C | p.Ala315Pro | missense_variant | 10/13 | 5 | A1 | ||
RTKN | ENST00000640304.2 | c.982G>C | p.Ala328Pro | missense_variant | 9/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251454Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135904
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 42AN XY: 727242
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2021 | The c.982G>C (p.A328P) alteration is located in exon 9 (coding exon 9) of the RTKN gene. This alteration results from a G to C substitution at nucleotide position 982, causing the alanine (A) at amino acid position 328 to be replaced by a proline (P). 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