5-159017266-C-T

Position:

• chr5-159017266-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024007.5(EBF1):​c.554+56130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,146 control chromosomes in the GnomAD database, including 7,057 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 0.29 (7057 hom., cov: 33)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EBF1	NM_024007.5	c.554+56130G>A		intron_variant		ENST00000313708.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EBF1	ENST00000313708.11	c.554+56130G>A		intron_variant		1	NM_024007.5	P1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44382 AN: 152028 Hom.: 7053 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.292 AC: 44404 AN: 152146 Hom.: 7057 Cov.: 33 AF XY: 0.292 AC XY: 21698 AN XY: 74392

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.0961

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.285

Alfa AF: 0.322 Hom.: 1642

Bravo AF: 0.276

Asia WGS AF: 0.174 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.3
DANN	Benign	0.82

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: rs36071027; hg19: chr5-158444274;