19-10320707-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_133452.3(RAVER1):c.1718G>A(p.Arg573His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000091 in 1,538,642 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_133452.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAVER1 | ENST00000617231.5 | c.1718G>A | p.Arg573His | missense_variant | Exon 9 of 13 | 5 | NM_133452.3 | ENSP00000482277.1 | ||
ENSG00000267303 | ENST00000586529.1 | n.-29G>A | upstream_gene_variant | 5 | ENSP00000467814.1 |
Frequencies
GnomAD3 genomes AF: 0.00000676 AC: 1AN: 147946Hom.: 0 Cov.: 28
GnomAD4 exome AF: 0.00000935 AC: 13AN: 1390696Hom.: 0 Cov.: 34 AF XY: 0.00000726 AC XY: 5AN XY: 688722
GnomAD4 genome AF: 0.00000676 AC: 1AN: 147946Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 71840
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1769G>A (p.R590H) alteration is located in exon 9 (coding exon 9) of the RAVER1 gene. This alteration results from a G to A substitution at nucleotide position 1769, causing the arginine (R) at amino acid position 590 to be replaced by a histidine (H). 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