chr5-158828038-T-A

Variant names:

• chr5-158828038-T-A
• rs1368297
• NM_024007.5:c.637-4721A>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.637-4721A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,942 control chromosomes in the GnomAD database, including 26,541 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 0.59 (26541 hom., cov: 32)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.68 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.637-4721A>T		intron	N/A	NP_076870.1	Q9UH73-1
	EBF1	NM_001324101.2		c.637-4721A>T		intron	N/A	NP_001311030.1
	EBF1	NM_001324103.2		c.637-4721A>T		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.637-4721A>T		intron	N/A	ENSP00000322898.6	Q9UH73-1
	EBF1	ENST00000380654.8	TSL:1	c.568-4721A>T		intron	N/A	ENSP00000370029.4	Q9UH73-2
	EBF1	ENST00000964682.1		c.760-4721A>T		intron	N/A	ENSP00000634741.1

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89451 AN: 151824 Hom.: 26524 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.589 AC: 89500 AN: 151942 Hom.: 26541 Cov.: 32 AF XY: 0.589 AC XY: 43741 AN XY: 74250

African (AFR) AF: 0.575 AC: 23844 AN: 41446

American (AMR) AF: 0.492 AC: 7508 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2013 AN: 3466

East Asian (EAS) AF: 0.537 AC: 2777 AN: 5174

South Asian (SAS) AF: 0.700 AC: 3369 AN: 4812

European-Finnish (FIN) AF: 0.637 AC: 6719 AN: 10554

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41357 AN: 67904

Other (OTH) AF: 0.567 AC: 1196 AN: 2108

Alfa AF: 0.609 Hom.: 3539

Bravo AF: 0.576

Asia WGS AF: 0.593 AC: 2060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.57
PhyloP100		0.083
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: rs1368297; hg19: chr5-158255046;