5-158852630-G-A

Position:

• chr5-158852630-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EBF1	NM_024007.5	c.555-12520C>T		intron_variant		ENST00000313708.11	NP_076870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EBF1	ENST00000313708.11	c.555-12520C>T		intron_variant		1	NM_024007.5	ENSP00000322898	P1

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

Gnomad4 AFR AF: 0.0466

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.211

Alfa AF: 0.268 Hom.: 3734

Bravo AF: 0.197

Asia WGS AF: 0.328 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	16
DANN	Benign	0.81

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

Publications

LitVar

Other links and lift over

dbSNP: rs891903; hg19: chr5-158279638;