rs929626

Variant names:

• chr5-158883623-A-G
• rs929626
• NM_024007.5:c.555-43513T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024007.5(EBF1):​c.555-43513T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,772 control chromosomes in the GnomAD database, including 12,950 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 0.41 (12950 hom., cov: 30)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.858
• Publications: 18 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.625 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBF1	NM_024007.5	MANE Select	c.555-43513T>C		intron	N/A	NP_076870.1
	EBF1	NM_001324101.2		c.555-43513T>C		intron	N/A	NP_001311030.1
	EBF1	NM_001324103.2		c.555-43513T>C		intron	N/A	NP_001311032.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBF1	ENST00000313708.11	TSL:1 MANE Select	c.555-43513T>C		intron	N/A	ENSP00000322898.6
	EBF1	ENST00000380654.8	TSL:1	c.486-43513T>C		intron	N/A	ENSP00000370029.4
	EBF1	ENST00000964682.1		c.678-43513T>C		intron	N/A	ENSP00000634741.1

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61563 AN: 151652 Hom.: 12934 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.406 AC: 61600 AN: 151772 Hom.: 12950 Cov.: 30 AF XY: 0.405 AC XY: 30027 AN XY: 74154

African (AFR) AF: 0.313 AC: 12934 AN: 41386

American (AMR) AF: 0.409 AC: 6241 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1543 AN: 3464

East Asian (EAS) AF: 0.321 AC: 1655 AN: 5150

South Asian (SAS) AF: 0.644 AC: 3097 AN: 4808

European-Finnish (FIN) AF: 0.350 AC: 3680 AN: 10508

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31017 AN: 67902

Other (OTH) AF: 0.408 AC: 858 AN: 2102

Alfa AF: 0.449 Hom.: 31691

Bravo AF: 0.403

Asia WGS AF: 0.452 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.54
PhyloP100		0.86
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: rs929626; hg19: chr5-158310631;