12-88046899-G-C
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001009894.3(RLIG1):c.712G>C(p.Val238Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 1,611,880 control chromosomes in the GnomAD database, including 272,810 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001009894.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RLIG1 | NM_001009894.3 | c.712G>C | p.Val238Leu | missense_variant | Exon 6 of 7 | ENST00000356891.4 | NP_001009894.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.497 AC: 75318AN: 151686Hom.: 20982 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.589 AC: 147567AN: 250530 AF XY: 0.596 show subpopulations
GnomAD4 exome AF: 0.583 AC: 851547AN: 1460076Hom.: 251824 Cov.: 39 AF XY: 0.586 AC XY: 425638AN XY: 726326 show subpopulations
GnomAD4 genome AF: 0.496 AC: 75327AN: 151804Hom.: 20986 Cov.: 31 AF XY: 0.502 AC XY: 37202AN XY: 74176 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at