5-159061190-A-C

Variant names:

• chr5-159061190-A-C
• rs929779
• NM_024007.5:c.554+12206T>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+12206T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,846 control chromosomes in the GnomAD database, including 15,665 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 0.44 (15665 hom., cov: 30)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594
• Publications: 7 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=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 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+12206T>G		intron	N/A	NP_076870.1
	EBF1	NM_001324101.2		c.554+12206T>G		intron	N/A	NP_001311030.1
	EBF1	NM_001324103.2		c.554+12206T>G		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+12206T>G		intron	N/A	ENSP00000322898.6
	EBF1	ENST00000380654.8	TSL:1	c.485+23476T>G		intron	N/A	ENSP00000370029.4
	EBF1	ENST00000517373.1	TSL:5	c.554+12206T>G		intron	N/A	ENSP00000428020.1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66607 AN: 151726 Hom.: 15663 Cov.: 30

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.439 AC: 66627 AN: 151846 Hom.: 15665 Cov.: 30 AF XY: 0.445 AC XY: 33029 AN XY: 74190

African (AFR) AF: 0.287 AC: 11874 AN: 41412

American (AMR) AF: 0.392 AC: 5992 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1560 AN: 3464

East Asian (EAS) AF: 0.242 AC: 1247 AN: 5160

South Asian (SAS) AF: 0.483 AC: 2318 AN: 4802

European-Finnish (FIN) AF: 0.657 AC: 6892 AN: 10498

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35268 AN: 67932

Other (OTH) AF: 0.434 AC: 910 AN: 2096

Alfa AF: 0.483 Hom.: 29505

Bravo AF: 0.408

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	20
DANN	Benign	0.72
PhyloP100		0.59
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: rs929779; hg19: chr5-158488198;