chr1-183883869-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001297671.3(RGL1):c.694T>C(p.Ser232Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000263 in 1,613,996 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
NM_001297671.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RGL1 | NM_001297671.3 | c.694T>C | p.Ser232Pro | missense_variant | 6/18 | ENST00000360851.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGL1 | ENST00000360851.4 | c.694T>C | p.Ser232Pro | missense_variant | 6/18 | 1 | NM_001297671.3 | P1 | |
RGL1 | ENST00000304685.8 | c.799T>C | p.Ser267Pro | missense_variant | 7/19 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000401 AC: 61AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000323 AC: 81AN: 251038Hom.: 0 AF XY: 0.000295 AC XY: 40AN XY: 135646
GnomAD4 exome AF: 0.000249 AC: 364AN: 1461776Hom.: 0 Cov.: 32 AF XY: 0.000270 AC XY: 196AN XY: 727196
GnomAD4 genome ? AF: 0.000401 AC: 61AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.799T>C (p.S267P) alteration is located in exon 7 (coding exon 6) of the RGL1 gene. This alteration results from a T to C substitution at nucleotide position 799, causing the serine (S) at amino acid position 267 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