chr14-100845451-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The ENST00000398461.5(MEG3):n.3046-7G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 456,600 control chromosomes in the GnomAD database, including 238 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
ENST00000398461.5 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MEG3 | NR_002766.2 | n.1184-7G>C | splice_region_variant, intron_variant | Intron 5 of 6 | ||||
MEG3 | NR_003530.2 | n.1434-7G>C | splice_region_variant, intron_variant | Intron 7 of 8 | ||||
MEG3 | NR_003531.3 | n.1301-7G>C | splice_region_variant, intron_variant | Intron 6 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MEG3 | ENST00000398461.5 | n.3046-7G>C | splice_region_variant, intron_variant | Intron 2 of 3 | 1 | |||||
MEG3 | ENST00000429159.6 | n.1200-7G>C | splice_region_variant, intron_variant | Intron 5 of 6 | 1 | |||||
MEG3 | ENST00000451743.6 | n.1166-7G>C | splice_region_variant, intron_variant | Intron 5 of 6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0173 AC: 2637AN: 152140Hom.: 43 Cov.: 32
GnomAD3 exomes AF: 0.0299 AC: 4127AN: 138068Hom.: 149 AF XY: 0.0255 AC XY: 1907AN XY: 74814
GnomAD4 exome AF: 0.0234 AC: 7132AN: 304342Hom.: 192 Cov.: 0 AF XY: 0.0203 AC XY: 3522AN XY: 173286
GnomAD4 genome AF: 0.0174 AC: 2648AN: 152258Hom.: 46 Cov.: 32 AF XY: 0.0159 AC XY: 1187AN XY: 74448
ClinVar
Submissions by phenotype
MEG3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at