6-130055161-C-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_032438.4(L3MBTL3):c.583-10C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000703 in 1,610,676 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00038 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00074 ( 1 hom. )
Consequence
L3MBTL3
NM_032438.4 intron
NM_032438.4 intron
Scores
2
Splicing: ADA: 0.0003290
2
Clinical Significance
Conservation
PhyloP100: 0.177
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 6-130055161-C-A is Benign according to our data. Variant chr6-130055161-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 732722.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 58 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
L3MBTL3 | NM_032438.4 | c.583-10C>A | intron_variant | ENST00000361794.7 | NP_115814.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
L3MBTL3 | ENST00000361794.7 | c.583-10C>A | intron_variant | 5 | NM_032438.4 | ENSP00000354526.2 |
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152184Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000338 AC: 85AN: 251304Hom.: 0 AF XY: 0.000353 AC XY: 48AN XY: 135830
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GnomAD4 exome AF: 0.000736 AC: 1074AN: 1458492Hom.: 1 Cov.: 29 AF XY: 0.000701 AC XY: 509AN XY: 725840
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GnomAD4 genome AF: 0.000381 AC: 58AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74342
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 26, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
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