5-159061190-A-C

Position:

• chr5-159061190-A-C

Variant summary

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

The NM_024007.5(EBF1):​c.554+12206T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,846 control chromosomes in the GnomAD database, including 15,665 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 0.44 (15665 hom., cov: 30)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594

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=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EBF1	NM_024007.5	c.554+12206T>G		intron_variant		ENST00000313708.11	NP_076870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EBF1	ENST00000313708.11	c.554+12206T>G		intron_variant		1	NM_024007.5	ENSP00000322898	P1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66607 AN: 151726 Hom.: 15663 Cov.: 30

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.439 AC: 66627 AN: 151846 Hom.: 15665 Cov.: 30 AF XY: 0.445 AC XY: 33029 AN XY: 74190

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.434

Alfa AF: 0.491 Hom.: 23621

Bravo AF: 0.408

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	20
DANN	Benign	0.72

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: rs929779; hg19: chr5-158488198;