5-158723638-T-C

Variant names:

• chr5-158723638-T-C
• rs7716399
• NM_024007.5:c.1125+7431A>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.1125+7431A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,092 control chromosomes in the GnomAD database, including 55,372 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 0.85 (55372 hom., cov: 30)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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.1125+7431A>G		intron	N/A	NP_076870.1
	EBF1	NM_001324101.2		c.1128+7431A>G		intron	N/A	NP_001311030.1
	EBF1	NM_001324103.2		c.1125+7431A>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.1125+7431A>G		intron	N/A	ENSP00000322898.6
	EBF1	ENST00000380654.8	TSL:1	c.1032+7431A>G		intron	N/A	ENSP00000370029.4
	EBF1	ENST00000517373.1	TSL:5	c.1101+7431A>G		intron	N/A	ENSP00000428020.1

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129488 AN: 151974 Hom.: 55325 Cov.: 30

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.852 AC: 129592 AN: 152092 Hom.: 55372 Cov.: 30 AF XY: 0.856 AC XY: 63634 AN XY: 74338

African (AFR) AF: 0.905 AC: 37540 AN: 41470

American (AMR) AF: 0.858 AC: 13102 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3000 AN: 3470

East Asian (EAS) AF: 0.985 AC: 5106 AN: 5182

South Asian (SAS) AF: 0.882 AC: 4256 AN: 4824

European-Finnish (FIN) AF: 0.838 AC: 8853 AN: 10564

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54825 AN: 67996

Other (OTH) AF: 0.861 AC: 1819 AN: 2112

Alfa AF: 0.817 Hom.: 37539

Bravo AF: 0.855

Asia WGS AF: 0.932 AC: 3242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.75
DANN	Benign	0.38
PhyloP100		-0.93
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: rs7716399; hg19: chr5-158150646;