rs11135910

chr8-26034626-C-T

Variant summary

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

The NM_022659.4(EBF2):c.483-1473G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,238 control chromosomes in the GnomAD database, including 1,492 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 0.13 (1492 hom., cov: 33)
• Consequence: EBF2 NM_022659.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

EBF2 (HGNC:19090): (EBF transcription factor 2) The protein encoded by this gene belongs to the COE (Collier/Olf/EBF) family of non-basic, helix-loop-helix transcription factors that have a well conserved DNA binding domain. The COE family proteins play an important role in variety of developmental processes. Studies in mouse suggest that this gene may be involved in the differentiation of osteoblasts. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EBF2	NM_022659.4	c.483-1473G>A		intron_variant		ENST00000520164.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EBF2	ENST00000520164.6	c.483-1473G>A		intron_variant		2	NM_022659.4	P1
EBF2	ENST00000517825.1	n.802-1473G>A		intron_variant, non_coding_transcript_variant		1
EBF2	ENST00000408929.7	c.39-1473G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20364 AN: 152120 Hom.: 1487 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.134 AC: 20387 AN: 152238 Hom.: 1492 Cov.: 33 AF XY: 0.130 AC XY: 9672 AN XY: 74440

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0948

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.134

Alfa AF: 0.154 Hom.: 2697

Bravo AF: 0.137

Asia WGS AF: 0.133 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	5.3
Dann	Benign	0.61

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: rs11135910; hg19: chr8-25892142;