ENST00000398461.5:n.3121+1333_3121+1334delGA
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The ENST00000398461.5(MEG3):n.3121+1333_3121+1334delGA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00206 in 152,350 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
ENST00000398461.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MEG3 | NR_046473.1 | n.2250_2251delGA | non_coding_transcript_exon_variant | Exon 7 of 7 | ||||
MEG3 | NR_190994.1 | n.2360_2361delGA | non_coding_transcript_exon_variant | Exon 8 of 8 | ||||
MEG3 | NR_190995.1 | n.2490_2491delGA | non_coding_transcript_exon_variant | Exon 9 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MEG3 | ENST00000398461.5 | n.3121+1333_3121+1334delGA | intron_variant | Intron 3 of 3 | 1 | |||||
MEG3 | ENST00000429159.6 | n.1275+1333_1275+1334delGA | intron_variant | Intron 6 of 6 | 1 | |||||
MEG3 | ENST00000451743.6 | n.1241+1333_1241+1334delGA | intron_variant | Intron 6 of 6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00204 AC: 311AN: 152232Hom.: 2 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 6Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 2
GnomAD4 genome AF: 0.00206 AC: 314AN: 152350Hom.: 2 Cov.: 32 AF XY: 0.00204 AC XY: 152AN XY: 74506
ClinVar
Submissions by phenotype
MEG3-related disorder Benign:1
This variant is classified as likely 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