chr9-20414378-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_004529.4(MLLT3):āc.468T>Cā(p.Ser156=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0807 in 144,612 control chromosomes in the GnomAD database, including 468 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.081 ( 468 hom., cov: 32)
Exomes š: 0.030 ( 965 hom. )
Failed GnomAD Quality Control
Consequence
MLLT3
NM_004529.4 synonymous
NM_004529.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.08
Genes affected
MLLT3 (HGNC:7136): (MLLT3 super elongation complex subunit) Enables chromatin binding activity and lysine-acetylated histone binding activity. Involved in several processes, including hematopoietic stem cell differentiation; positive regulation of transcription, DNA-templated; and regulation of stem cell division. Acts upstream of or within negative regulation of canonical Wnt signaling pathway and positive regulation of Wnt signaling pathway, planar cell polarity pathway. Located in cytosol and nucleoplasm. Part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 9-20414378-A-G is Benign according to our data. Variant chr9-20414378-A-G is described in ClinVar as [Benign]. Clinvar id is 770580.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.08 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0882 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLLT3 | NM_004529.4 | c.468T>C | p.Ser156= | synonymous_variant | 5/11 | ENST00000380338.9 | |
MLLT3 | NM_001286691.2 | c.459T>C | p.Ser153= | synonymous_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLLT3 | ENST00000380338.9 | c.468T>C | p.Ser156= | synonymous_variant | 5/11 | 1 | NM_004529.4 | P4 | |
MLLT3 | ENST00000630269.2 | c.459T>C | p.Ser153= | synonymous_variant | 5/11 | 2 | A1 | ||
MLLT3 | ENST00000475957.1 | n.425T>C | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0806 AC: 11653AN: 144494Hom.: 468 Cov.: 32
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GnomAD3 exomes AF: 0.0295 AC: 5146AN: 174546Hom.: 146 AF XY: 0.0269 AC XY: 2574AN XY: 95678
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0298 AC: 37301AN: 1250356Hom.: 965 Cov.: 34 AF XY: 0.0320 AC XY: 20004AN XY: 625116
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.0807 AC: 11668AN: 144612Hom.: 468 Cov.: 32 AF XY: 0.0791 AC XY: 5585AN XY: 70584
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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 | Nov 30, 2017 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at