rs17717527

chr5-159039275-T-Achr5-159039275-T-G

Variant summary

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

The NM_024007.5(EBF1):c.554+34121A>T variant causes a intron change. The variant allele was found at a frequency of 0.347 in 152,104 control chromosomes in the GnomAD database, including 10,214 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 0.35 (10214 hom., cov: 32)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.87

Genes affected

EBF1 (HGNC:3126): (EBF transcription factor 1) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of transcription, DNA-templated. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EBF1	NM_024007.5	c.554+34121A>T		intron_variant		ENST00000313708.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EBF1	ENST00000313708.11	c.554+34121A>T		intron_variant		1	NM_024007.5	P1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52720 AN: 151984 Hom.: 10215 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.347 AC: 52720 AN: 152104 Hom.: 10214 Cov.: 32 AF XY: 0.354 AC XY: 26330 AN XY: 74346

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.332

Alfa AF: 0.273 Hom.: 734

Bravo AF: 0.316

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	16
Dann	Benign	0.65

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: rs17717527; hg19: chr5-158466283;