10-129887408-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001375380.1(EBF3):​c.555-9559A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,048 control chromosomes in the GnomAD database, including 17,786 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.47 ( 17786 hom., cov: 33)

Consequence

EBF3
NM_001375380.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.483
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.25).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EBF3NM_001375380.1 linkc.555-9559A>G intron_variant ENST00000440978.2 NP_001362309.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EBF3ENST00000440978.2 linkc.555-9559A>G intron_variant 3 NM_001375380.1 ENSP00000387543.2 H0Y3W9

Frequencies

GnomAD3 genomes
AF:
0.471
AC:
71572
AN:
151930
Hom.:
17782
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.639
Gnomad AMI
AF:
0.390
Gnomad AMR
AF:
0.437
Gnomad ASJ
AF:
0.374
Gnomad EAS
AF:
0.506
Gnomad SAS
AF:
0.392
Gnomad FIN
AF:
0.394
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.398
Gnomad OTH
AF:
0.442
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.471
AC:
71612
AN:
152048
Hom.:
17786
Cov.:
33
AF XY:
0.470
AC XY:
34929
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.639
Gnomad4 AMR
AF:
0.437
Gnomad4 ASJ
AF:
0.374
Gnomad4 EAS
AF:
0.506
Gnomad4 SAS
AF:
0.391
Gnomad4 FIN
AF:
0.394
Gnomad4 NFE
AF:
0.398
Gnomad4 OTH
AF:
0.441
Alfa
AF:
0.434
Hom.:
7391
Bravo
AF:
0.482
Asia WGS
AF:
0.460
AC:
1600
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.25
CADD
Benign
14
DANN
Benign
0.76

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs1334011; hg19: chr10-131685672; API