rs17717527

Variant names:

• chr5-159039275-T-A
• rs17717527
• NM_024007.5:c.554+34121A>T

Your query was ambiguous. Multiple possible variants found:

• chr5-159039275-T-A
• chr5-159039275-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024007.5. 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
	EBF1	NM_024007.5	MANE Select	c.554+34121A>T		intron	N/A	NP_076870.1
	EBF1	NM_001324101.2		c.554+34121A>T		intron	N/A	NP_001311030.1
	EBF1	NM_001324103.2		c.554+34121A>T		intron	N/A	NP_001311032.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBF1	ENST00000313708.11	TSL:1 MANE Select	c.554+34121A>T		intron	N/A	ENSP00000322898.6
	EBF1	ENST00000380654.8	TSL:1	c.485+45391A>T		intron	N/A	ENSP00000370029.4
	EBF1	ENST00000517373.1	TSL:5	c.554+34121A>T		intron	N/A	ENSP00000428020.1

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

African (AFR) AF: 0.176 AC: 7293 AN: 41498

American (AMR) AF: 0.314 AC: 4795 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1261 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1256 AN: 5180

South Asian (SAS) AF: 0.388 AC: 1869 AN: 4816

European-Finnish (FIN) AF: 0.568 AC: 6017 AN: 10588

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29043 AN: 67974

Other (OTH) AF: 0.332 AC: 699 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	16
DANN	Benign	0.65
PhyloP100		4.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17717527; hg19: chr5-158466283;