rs10040979

Variant names:

• chr5-158997383-G-A
• rs10040979
• NM_024007.5:c.554+76013C>T

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+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
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.779 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+76013C>T		intron	N/A	NP_076870.1
	EBF1	NM_001324101.2		c.554+76013C>T		intron	N/A	NP_001311030.1
	EBF1	NM_001324103.2		c.554+76013C>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+76013C>T		intron	N/A	ENSP00000322898.6
	EBF1	ENST00000380654.8	TSL:1	c.485+87283C>T		intron	N/A	ENSP00000370029.4
	EBF1	ENST00000517373.1	TSL:5	c.554+76013C>T		intron	N/A	ENSP00000428020.1

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

African (AFR) AF: 0.522 AC: 21615 AN: 41418

American (AMR) AF: 0.554 AC: 8460 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2119 AN: 3468

East Asian (EAS) AF: 0.401 AC: 2072 AN: 5162

South Asian (SAS) AF: 0.800 AC: 3855 AN: 4818

European-Finnish (FIN) AF: 0.609 AC: 6435 AN: 10562

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46243 AN: 67966

Other (OTH) AF: 0.598 AC: 1261 AN: 2110

Alfa AF: 0.655 Hom.: 60786

Bravo AF: 0.596

Asia WGS AF: 0.575 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.93
DANN	Benign	0.48
PhyloP100		0.10
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: rs10040979; hg19: chr5-158424391; COSMIC: COSV58180729;