5-158755322-C-T

Variant names:

• chr5-158755322-C-T
• rs17712788
• NM_024007.5:c.1036+22091G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024007.5(EBF1):​c.1036+22091G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,022 control chromosomes in the GnomAD database, including 2,491 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 0.17 (2491 hom., cov: 32)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 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.1036+22091G>A		intron	N/A	NP_076870.1	Q9UH73-1
	EBF1	NM_001324101.2		c.1039+22091G>A		intron	N/A	NP_001311030.1
	EBF1	NM_001324103.2		c.1036+22091G>A		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.1036+22091G>A		intron	N/A	ENSP00000322898.6	Q9UH73-1
	EBF1	ENST00000380654.8	TSL:1	c.943+22091G>A		intron	N/A	ENSP00000370029.4	Q9UH73-2
	EBF1	ENST00000964682.1		c.1159+22091G>A		intron	N/A	ENSP00000634741.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25401 AN: 151904 Hom.: 2486 Cov.: 32

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.167 AC: 25416 AN: 152022 Hom.: 2491 Cov.: 32 AF XY: 0.165 AC XY: 12285 AN XY: 74302

African (AFR) AF: 0.0926 AC: 3840 AN: 41490

American (AMR) AF: 0.147 AC: 2242 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3468

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5164

South Asian (SAS) AF: 0.154 AC: 744 AN: 4818

European-Finnish (FIN) AF: 0.263 AC: 2781 AN: 10562

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14664 AN: 67942

Other (OTH) AF: 0.167 AC: 352 AN: 2110

Alfa AF: 0.192 Hom.: 7094

Bravo AF: 0.155

Asia WGS AF: 0.0800 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.72
PhyloP100		0.092
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: rs17712788; hg19: chr5-158182330; COSMIC: COSV58171798;