rs17818083

Positions:

• chr8-26012761-G-A
• chr8-26012761-G-C

Variant summary

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

The NM_022659.4(EBF2):​c.551+20324C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,206 control chromosomes in the GnomAD database, including 1,322 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 0.12 (1322 hom., cov: 32)
• Consequence: EBF2 NM_022659.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

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=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EBF2	NM_022659.4	c.551+20324C>T		intron_variant		ENST00000520164.6	NP_073150.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EBF2	ENST00000520164.6	c.551+20324C>T		intron_variant		2	NM_022659.4	ENSP00000430241.1
EBF2	ENST00000408929.7	c.107+20324C>T		intron_variant		2		ENSP00000386178.3

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17755 AN: 152086 Hom.: 1323 Cov.: 32

Gnomad AFR AF: 0.0357

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0947

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0923

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.117 AC: 17747 AN: 152206 Hom.: 1322 Cov.: 32 AF XY: 0.114 AC XY: 8516 AN XY: 74428

Gnomad4 AFR AF: 0.0356

Gnomad4 AMR AF: 0.0946

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0925

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.134

Alfa AF: 0.153 Hom.: 2893

Bravo AF: 0.111

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.1
DANN	Benign	0.88

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: rs17818083; hg19: chr8-25870277;