1-100273401-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003729.4(RTCA):c.422A>G(p.Lys141Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000209 in 1,581,024 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_003729.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RTCA | ENST00000370128.9 | c.422A>G | p.Lys141Arg | missense_variant | Exon 5 of 11 | 1 | NM_003729.4 | ENSP00000359146.4 | ||
RTCA | ENST00000260563.4 | c.461A>G | p.Lys154Arg | missense_variant | Exon 6 of 12 | 1 | ENSP00000260563.4 | |||
RTCA | ENST00000483474.1 | n.632A>G | non_coding_transcript_exon_variant | Exon 6 of 6 | 3 | |||||
RTCA | ENST00000498617.5 | n.660A>G | non_coding_transcript_exon_variant | Exon 5 of 6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000356 AC: 8AN: 224566Hom.: 0 AF XY: 0.0000330 AC XY: 4AN XY: 121120
GnomAD4 exome AF: 0.0000217 AC: 31AN: 1428822Hom.: 0 Cov.: 26 AF XY: 0.0000197 AC XY: 14AN XY: 709992
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.461A>G (p.K154R) alteration is located in exon 6 (coding exon 6) of the RTCA gene. This alteration results from a A to G substitution at nucleotide position 461, causing the lysine (K) at amino acid position 154 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at