14-100831954-T-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000452120.7(MEG3):n.3130T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00791 in 152,034 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0079 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MEG3
ENST00000452120.7 non_coding_transcript_exon
ENST00000452120.7 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.232
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 14-100831954-T-G is Benign according to our data. Variant chr14-100831954-T-G is described in ClinVar as [Benign]. Clinvar id is 2644540.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 9 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MEG3 | NR_002766.2 | n.1049+420T>G | intron_variant | |||||
MEG3 | NR_003530.2 | n.1049+420T>G | intron_variant | |||||
MEG3 | NR_003531.3 | n.1025+420T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MEG3 | ENST00000429159.6 | n.936-558T>G | intron_variant | 1 | ||||||
MEG3 | ENST00000451743.6 | n.1031+420T>G | intron_variant | 1 | ||||||
MEG3 | ENST00000521404.5 | n.917+2205T>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00791 AC: 1202AN: 151916Hom.: 9 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 10Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 4
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GnomAD4 genome AF: 0.00791 AC: 1202AN: 152034Hom.: 9 Cov.: 32 AF XY: 0.00721 AC XY: 536AN XY: 74306
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | MEG3: BS1, BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at