NM_001375380.1:c.1038C>A

Variant names:

• chr10-129867142-G-T
• rs142165671
• NM_001375380.1:c.1038C>A

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001375380.1(EBF3):​c.1038C>A​(p.Thr346Thr) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T346T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: EBF3 NM_001375380.1 splice_region, synonymous
• Scores: Splicing: ADA: 0.0001322
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 2 publications found

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]

EBF3-AS1 (HGNC:56218): (EBF3 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP7: Synonymous conserved (PhyloP=-0.885 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375380.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBF3	NM_001375380.1	MANE Select	c.1038C>A	p.Thr346Thr	splice_region synonymous	Exon 10 of 17	NP_001362309.1
	EBF3	NM_001375379.1		c.1038C>A	p.Thr346Thr	splice_region synonymous	Exon 10 of 16	NP_001362308.1
	EBF3	NM_001375389.1		c.1038C>A	p.Thr346Thr	splice_region synonymous	Exon 10 of 17	NP_001362318.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBF3	ENST00000440978.2	TSL:3 MANE Select	c.1038C>A	p.Thr346Thr	splice_region synonymous	Exon 10 of 17	ENSP00000387543.2
	EBF3	ENST00000368648.8	TSL:1	c.1011C>A	p.Thr337Thr	splice_region synonymous	Exon 11 of 17	ENSP00000357637.3
	EBF3	ENST00000355311.10	TSL:5	c.1038C>A	p.Thr346Thr	splice_region synonymous	Exon 10 of 16	ENSP00000347463.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	0.91
DANN	Benign	0.84
PhyloP100		-0.89

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00013
dbscSNV1_RF	Benign	0.11
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

Other links and lift over

dbSNP: rs142165671; hg19: chr10-131665406;