rs10515789

Positions:

• chr5-159079407-T-G

Variant summary

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

The NM_024007.5(EBF1):​c.485+5259A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,116 control chromosomes in the GnomAD database, including 1,172 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 0.11 (1172 hom., cov: 31)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EBF1	NM_024007.5	c.485+5259A>C		intron_variant		ENST00000313708.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EBF1	ENST00000313708.11	c.485+5259A>C		intron_variant		1	NM_024007.5	P1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16472 AN: 151998 Hom.: 1166 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0746

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.108 AC: 16497 AN: 152116 Hom.: 1172 Cov.: 31 AF XY: 0.110 AC XY: 8212 AN XY: 74384

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0746

Gnomad4 NFE AF: 0.0652

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0757 Hom.: 593

Bravo AF: 0.121

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.53

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: rs10515789; hg19: chr5-158506415;