1-100273398-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_003729.4(RTCA):c.419T>C(p.Phe140Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000443 in 1,578,578 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003729.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RTCA | ENST00000370128.9 | c.419T>C | p.Phe140Ser | missense_variant | Exon 5 of 11 | 1 | NM_003729.4 | ENSP00000359146.4 | ||
RTCA | ENST00000260563.4 | c.458T>C | p.Phe153Ser | missense_variant | Exon 6 of 12 | 1 | ENSP00000260563.4 | |||
RTCA | ENST00000483474.1 | n.629T>C | non_coding_transcript_exon_variant | Exon 6 of 6 | 3 | |||||
RTCA | ENST00000498617.5 | n.657T>C | non_coding_transcript_exon_variant | Exon 5 of 6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000351 AC: 5AN: 1426362Hom.: 0 Cov.: 26 AF XY: 0.00000423 AC XY: 3AN XY: 708832
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.458T>C (p.F153S) alteration is located in exon 6 (coding exon 6) of the RTCA gene. This alteration results from a T to C substitution at nucleotide position 458, causing the phenylalanine (F) at amino acid position 153 to be replaced by a serine (S). 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