chr5-159048203-C-T

Variant names:

• chr5-159048203-C-T
• rs10515787
• NM_024007.5:c.554+25193G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024007.5(EBF1):​c.554+25193G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0454 in 152,244 control chromosomes in the GnomAD database, including 630 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 0.045 (630 hom., cov: 32)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 6 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EBF1	NM_024007.5	c.554+25193G>A		intron_variant	Intron 6 of 15	ENST00000313708.11	NP_076870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EBF1	ENST00000313708.11	c.554+25193G>A		intron_variant	Intron 6 of 15	1	NM_024007.5	ENSP00000322898.6

Frequencies

GnomAD3 genomes AF: 0.0454 AC: 6899 AN: 152126 Hom.: 629 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0588

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

GnomAD4 genome AF: 0.0454 AC: 6907 AN: 152244 Hom.: 630 Cov.: 32 AF XY: 0.0510 AC XY: 3799 AN XY: 74430

African (AFR) AF: 0.0181 AC: 753 AN: 41550

American (AMR) AF: 0.135 AC: 2058 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3466

East Asian (EAS) AF: 0.379 AC: 1957 AN: 5164

South Asian (SAS) AF: 0.0823 AC: 397 AN: 4824

European-Finnish (FIN) AF: 0.0388 AC: 411 AN: 10606

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0153 AC: 1040 AN: 68020

Other (OTH) AF: 0.0601 AC: 127 AN: 2114

Alfa AF: 0.0315 Hom.: 709

Bravo AF: 0.0543

Asia WGS AF: 0.224 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.9
DANN	Benign	0.75
PhyloP100		0.053
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: rs10515787; hg19: chr5-158475211;