2-74426338-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001015055.2(RTKN):c.1597C>T(p.Arg533Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,268 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 (★).
Frequency
Consequence
NM_001015055.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTKN | NM_001015055.2 | c.1597C>T | p.Arg533Cys | missense_variant | 12/12 | ENST00000272430.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTKN | ENST00000272430.10 | c.1597C>T | p.Arg533Cys | missense_variant | 12/12 | 1 | NM_001015055.2 | P4 | |
RTKN | ENST00000233330.6 | c.1447C>T | p.Arg483Cys | missense_variant | 12/12 | 1 | |||
RTKN | ENST00000305557.9 | c.1558C>T | p.Arg520Cys | missense_variant | 13/13 | 5 | A1 | ||
RTKN | ENST00000640304.2 | c.*309C>T | 3_prime_UTR_variant | 12/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246640Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134104
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1460956Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726804
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 19, 2023 | The c.1597C>T (p.R533C) alteration is located in exon 12 (coding exon 12) of the RTKN gene. This alteration results from a C to T substitution at nucleotide position 1597, causing the arginine (R) at amino acid position 533 to be replaced by a cysteine (C). 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