chr20-43515316-A-G
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001377303.1(L3MBTL1):āc.678A>Gā(p.Ser226Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000009 in 1,444,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.0000090 ( 0 hom. )
Consequence
L3MBTL1
NM_001377303.1 synonymous
NM_001377303.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.402
Genes affected
L3MBTL1 (HGNC:15905): (L3MBTL histone methyl-lysine binding protein 1) This gene represents a polycomb group gene. The encoded protein functions to regulate gene activity, likely via chromatin modification. The encoded protein may also be necessary for mitosis. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 20-43515316-A-G is Benign according to our data. Variant chr20-43515316-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2652345.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.402 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
L3MBTL1 | NM_001377303.1 | c.678A>G | p.Ser226Ser | synonymous_variant | 6/22 | ENST00000418998.7 | NP_001364232.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
L3MBTL1 | ENST00000418998.7 | c.678A>G | p.Ser226Ser | synonymous_variant | 6/22 | 2 | NM_001377303.1 | ENSP00000398516.2 | ||
ENSG00000288000 | ENST00000657241.1 | c.1359A>G | p.Ser453Ser | synonymous_variant | 10/26 | ENSP00000499734.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000900 AC: 13AN: 1444898Hom.: 0 Cov.: 32 AF XY: 0.0000125 AC XY: 9AN XY: 717224
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717224
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GnomAD4 genome Cov.: 33
GnomAD4 genome
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33
Bravo
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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 | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | L3MBTL1: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at