5-158852630-G-A

Variant names:

• chr5-158852630-G-A
• rs891903
• NM_024007.5:c.555-12520C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024007.5(EBF1):​c.555-12520C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,078 control chromosomes in the GnomAD database, including 4,184 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 0.21 (4184 hom., cov: 32)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 9 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 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.555-12520C>T		intron	N/A	NP_076870.1
	EBF1	NM_001324101.2		c.555-12520C>T		intron	N/A	NP_001311030.1
	EBF1	NM_001324103.2		c.555-12520C>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.555-12520C>T		intron	N/A	ENSP00000322898.6
	EBF1	ENST00000380654.8	TSL:1	c.486-12520C>T		intron	N/A	ENSP00000370029.4
	EBF1	ENST00000517373.1	TSL:5	c.555-12520C>T		intron	N/A	ENSP00000428020.1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31233 AN: 151960 Hom.: 4186 Cov.: 32

Gnomad AFR AF: 0.0467

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.205 AC: 31226 AN: 152078 Hom.: 4184 Cov.: 32 AF XY: 0.208 AC XY: 15441 AN XY: 74326

African (AFR) AF: 0.0466 AC: 1932 AN: 41482

American (AMR) AF: 0.226 AC: 3456 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1085 AN: 3472

East Asian (EAS) AF: 0.262 AC: 1360 AN: 5184

South Asian (SAS) AF: 0.493 AC: 2371 AN: 4808

European-Finnish (FIN) AF: 0.210 AC: 2216 AN: 10558

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17955 AN: 67970

Other (OTH) AF: 0.211 AC: 446 AN: 2114

Alfa AF: 0.265 Hom.: 5055

Bravo AF: 0.197

Asia WGS AF: 0.328 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	16
DANN	Benign	0.81
PhyloP100		0.18
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: rs891903; hg19: chr5-158279638;