chr1-183883800-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001297671.3(RGL1):c.625A>G(p.Thr209Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,614,088 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.625A>G | p.Thr209Ala | missense_variant | 6/18 | ENST00000360851.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGL1 | ENST00000360851.4 | c.625A>G | p.Thr209Ala | missense_variant | 6/18 | 1 | NM_001297671.3 | P1 | |
RGL1 | ENST00000304685.8 | c.730A>G | p.Thr244Ala | missense_variant | 7/19 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000123 AC: 31AN: 251102Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135690
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461748Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727190
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.730A>G (p.T244A) alteration is located in exon 7 (coding exon 6) of the RGL1 gene. This alteration results from a A to G substitution at nucleotide position 730, causing the threonine (T) at amino acid position 244 to be replaced by an alanine (A). 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