ENST00000609883.3:c.1429G>C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000609883.3(RTL5):c.1429G>C(p.Ala477Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000438 in 1,208,690 control chromosomes in the GnomAD database, including 1 homozygotes. There are 20 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A477T) has been classified as Likely benign.
Frequency
Consequence
ENST00000609883.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 16AN: 110519Hom.: 1 Cov.: 22 AF XY: 0.000122 AC XY: 4AN XY: 32721
GnomAD3 exomes AF: 0.0000826 AC: 15AN: 181652Hom.: 0 AF XY: 0.0000888 AC XY: 6AN XY: 67584
GnomAD4 exome AF: 0.0000337 AC: 37AN: 1098114Hom.: 0 Cov.: 34 AF XY: 0.0000440 AC XY: 16AN XY: 363540
GnomAD4 genome AF: 0.000145 AC: 16AN: 110576Hom.: 1 Cov.: 22 AF XY: 0.000122 AC XY: 4AN XY: 32788
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1429G>C (p.A477P) alteration is located in exon 1 (coding exon 1) of the RGAG4 gene. This alteration results from a G to C substitution at nucleotide position 1429, causing the alanine (A) at amino acid position 477 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