10-129840267-G-A
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001375380.1(EBF3):c.1737C>T(p.Ser579=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000194 in 1,584,790 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 Benign (★).
Frequency
Genomes: 𝑓 0.00028 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00018 ( 1 hom. )
Consequence
EBF3
NM_001375380.1 synonymous
NM_001375380.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.57
Genes affected
EBF3 (HGNC:19087): (EBF transcription factor 3) This gene encodes a member of the early B-cell factor (EBF) family of DNA binding transcription factors. EBF proteins are involved in B-cell differentiation, bone development and neurogenesis, and may also function as tumor suppressors. The encoded protein inhibits cell survival through the regulation of genes involved in cell cycle arrest and apoptosis, and aberrant methylation or deletion of this gene may play a role in multiple malignancies including glioblastoma multiforme and gastric carcinoma. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
Variant 10-129840267-G-A is Benign according to our data. Variant chr10-129840267-G-A is described in ClinVar as [Benign]. Clinvar id is 728632.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.57 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000282 (43/152330) while in subpopulation EAS AF= 0.00754 (39/5174). AF 95% confidence interval is 0.00567. There are 0 homozygotes in gnomad4. There are 23 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 43 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EBF3 | NM_001375380.1 | c.1737C>T | p.Ser579= | synonymous_variant | 15/17 | ENST00000440978.2 | NP_001362309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EBF3 | ENST00000440978.2 | c.1737C>T | p.Ser579= | synonymous_variant | 15/17 | 3 | NM_001375380.1 | ENSP00000387543 | ||
EBF3 | ENST00000368648.8 | c.1602C>T | p.Ser534= | synonymous_variant | 16/17 | 1 | ENSP00000357637 | A1 | ||
EBF3 | ENST00000355311.10 | c.1737C>T | p.Ser579= | synonymous_variant | 15/16 | 5 | ENSP00000347463 | P4 | ||
EBF3 | ENST00000675373.1 | n.1274C>T | non_coding_transcript_exon_variant | 12/14 |
Frequencies
GnomAD3 genomes AF: 0.000282 AC: 43AN: 152214Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000653 AC: 133AN: 203666Hom.: 0 AF XY: 0.000579 AC XY: 63AN XY: 108876
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GnomAD4 exome AF: 0.000185 AC: 265AN: 1432460Hom.: 1 Cov.: 37 AF XY: 0.000178 AC XY: 126AN XY: 709544
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GnomAD4 genome AF: 0.000282 AC: 43AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
EBF3-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
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