9-113462048-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000350696.9(RGS3):c.262C>T(p.Leu88Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,614,008 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
ENST00000350696.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RGS3 | NM_144488.8 | c.-51C>T | 5_prime_UTR_variant | 4/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGS3 | ENST00000350696.9 | c.262C>T | p.Leu88Phe | missense_variant | 3/25 | 5 | A2 | ||
RGS3 | ENST00000374140.6 | c.262C>T | p.Leu88Phe | missense_variant | 4/26 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152216Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000120 AC: 30AN: 249346Hom.: 0 AF XY: 0.0000961 AC XY: 13AN XY: 135246
GnomAD4 exome AF: 0.0000643 AC: 94AN: 1461674Hom.: 0 Cov.: 32 AF XY: 0.0000646 AC XY: 47AN XY: 727130
GnomAD4 genome AF: 0.0000656 AC: 10AN: 152334Hom.: 0 Cov.: 31 AF XY: 0.0000940 AC XY: 7AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.262C>T (p.L88F) alteration is located in exon 4 (coding exon 3) of the RGS3 gene. This alteration results from a C to T substitution at nucleotide position 262, causing the leucine (L) at amino acid position 88 to be replaced by a phenylalanine (F). 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