rs10040979

chr5-158997383-G-A

Variant summary

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

The NM_024007.5(EBF1):c.554+76013C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,982 control chromosomes in the GnomAD database, including 28,990 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 0.61 (28990 hom., cov: 31)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EBF1	NM_024007.5	c.554+76013C>T		intron_variant		ENST00000313708.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EBF1	ENST00000313708.11	c.554+76013C>T		intron_variant		1	NM_024007.5	P1

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92764 AN: 151862 Hom.: 28969 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.611 AC: 92832 AN: 151982 Hom.: 28990 Cov.: 31 AF XY: 0.607 AC XY: 45096 AN XY: 74276

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.598

Alfa AF: 0.664 Hom.: 44628

Bravo AF: 0.596

Asia WGS AF: 0.575 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.93
Dann	Benign	0.48

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: rs10040979; hg19: chr5-158424391; COSMIC: COSV58180729;