10-129840309-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001375380.1(EBF3):​c.1695C>T​(p.Pro565=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00174 in 1,591,842 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0018 ( 2 hom. )

Consequence

EBF3
NM_001375380.1 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.156
Variant links:
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 -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 10-129840309-G-A is Benign according to our data. Variant chr10-129840309-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 789310.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.156 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00119 (182/152362) while in subpopulation NFE AF= 0.00218 (148/68034). AF 95% confidence interval is 0.00189. There are 0 homozygotes in gnomad4. There are 70 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 182 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EBF3NM_001375380.1 linkuse as main transcriptc.1695C>T p.Pro565= synonymous_variant 15/17 ENST00000440978.2 NP_001362309.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EBF3ENST00000440978.2 linkuse as main transcriptc.1695C>T p.Pro565= synonymous_variant 15/173 NM_001375380.1 ENSP00000387543
EBF3ENST00000368648.8 linkuse as main transcriptc.1560C>T p.Pro520= synonymous_variant 16/171 ENSP00000357637 A1Q9H4W6-2
EBF3ENST00000355311.10 linkuse as main transcriptc.1695C>T p.Pro565= synonymous_variant 15/165 ENSP00000347463 P4Q9H4W6-1
EBF3ENST00000675373.1 linkuse as main transcriptn.1232C>T non_coding_transcript_exon_variant 12/14

Frequencies

GnomAD3 genomes
AF:
0.00120
AC:
182
AN:
152244
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000362
Gnomad AMI
AF:
0.00329
Gnomad AMR
AF:
0.000785
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00218
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000898
AC:
190
AN:
211674
Hom.:
0
AF XY:
0.000888
AC XY:
101
AN XY:
113680
show subpopulations
Gnomad AFR exome
AF:
0.000551
Gnomad AMR exome
AF:
0.000197
Gnomad ASJ exome
AF:
0.000216
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000380
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00184
Gnomad OTH exome
AF:
0.000561
GnomAD4 exome
AF:
0.00180
AC:
2589
AN:
1439480
Hom.:
2
Cov.:
37
AF XY:
0.00171
AC XY:
1217
AN XY:
713732
show subpopulations
Gnomad4 AFR exome
AF:
0.000271
Gnomad4 AMR exome
AF:
0.000387
Gnomad4 ASJ exome
AF:
0.000156
Gnomad4 EAS exome
AF:
0.000361
Gnomad4 SAS exome
AF:
0.0000849
Gnomad4 FIN exome
AF:
0.000136
Gnomad4 NFE exome
AF:
0.00223
Gnomad4 OTH exome
AF:
0.00121
GnomAD4 genome
AF:
0.00119
AC:
182
AN:
152362
Hom.:
0
Cov.:
33
AF XY:
0.000940
AC XY:
70
AN XY:
74506
show subpopulations
Gnomad4 AFR
AF:
0.000361
Gnomad4 AMR
AF:
0.000784
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00218
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.00117
Hom.:
0
Bravo
AF:
0.00127

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 31, 2019- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2024EBF3: BP4, BP7, BS1 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
CADD
Benign
10
DANN
Benign
0.90

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs148512369; hg19: chr10-131638573; API