chr6-130068424-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_032438.4(L3MBTL3):c.1092+3A>G variant causes a splice donor region, intron change. The variant allele was found at a frequency of 0.00327 in 1,510,126 control chromosomes in the GnomAD database, including 132 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.018 ( 73 hom., cov: 33)
Exomes 𝑓: 0.0017 ( 59 hom. )
Consequence
L3MBTL3
NM_032438.4 splice_donor_region, intron
NM_032438.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.9717
1
1
Clinical Significance
Conservation
PhyloP100: 4.52
Genes affected
L3MBTL3 (HGNC:23035): (L3MBTL histone methyl-lysine binding protein 3) This gene encodes a member of the malignant brain tumor (MBT) family of chromatin interacting transcriptional repressors. Members of this family function as methyl-lysine readers, which recognize methylated lysine residues on histone protein tails, and are associated with the repression of gene expression. The encoded protein may regulate hematopoiesis. Homozygous deletion of this gene has been observed in human patients with medulloblastoma. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.19).
BP6
?
Variant 6-130068424-A-G is Benign according to our data. Variant chr6-130068424-A-G is described in ClinVar as [Benign]. Clinvar id is 768109.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0585 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L3MBTL3 | NM_032438.4 | c.1092+3A>G | splice_donor_region_variant, intron_variant | ENST00000361794.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L3MBTL3 | ENST00000361794.7 | c.1092+3A>G | splice_donor_region_variant, intron_variant | 5 | NM_032438.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0175 AC: 2667AN: 152208Hom.: 73 Cov.: 33
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GnomAD3 exomes AF: 0.00446 AC: 1115AN: 249728Hom.: 30 AF XY: 0.00326 AC XY: 440AN XY: 135016
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GnomAD4 exome AF: 0.00168 AC: 2278AN: 1357800Hom.: 59 Cov.: 22 AF XY: 0.00142 AC XY: 965AN XY: 681588
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GnomAD4 genome ? AF: 0.0175 AC: 2666AN: 152326Hom.: 73 Cov.: 33 AF XY: 0.0175 AC XY: 1300AN XY: 74484
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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 | Invitae | Jul 26, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at