rs929626

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EBF1	NM_024007.5	c.555-43513T>C		intron_variant	Intron 6 of 15	ENST00000313708.11	NP_076870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EBF1	ENST00000313708.11	c.555-43513T>C		intron_variant	Intron 6 of 15	1	NM_024007.5	ENSP00000322898.6

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

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.408

Alfa AF: 0.453 Hom.: 23474

Bravo AF: 0.403

Asia WGS AF: 0.452 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.54

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: rs929626; hg19: chr5-158310631;