rs9804200

Positions:

• chr10-129875722-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375380.1(EBF3):​c.636+2046G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,154 control chromosomes in the GnomAD database, including 31,676 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 0.64 (31676 hom., cov: 33)
• Consequence: EBF3 NM_001375380.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EBF3	NM_001375380.1	c.636+2046G>A		intron_variant		ENST00000440978.2	NP_001362309.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EBF3	ENST00000440978.2	c.636+2046G>A		intron_variant		3	NM_001375380.1	ENSP00000387543

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97740 AN: 152036 Hom.: 31664 Cov.: 33

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.656

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.643 AC: 97785 AN: 152154 Hom.: 31676 Cov.: 33 AF XY: 0.639 AC XY: 47558 AN XY: 74378

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.651

Alfa AF: 0.684 Hom.: 34060

Bravo AF: 0.641

Asia WGS AF: 0.538 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.34

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

Other links and lift over

dbSNP: rs9804200; hg19: chr10-131673986;