chr5-158726070-G-A

Variant names:

• chr5-158726070-G-A
• rs17056131
• NM_024007.5:c.1125+4999C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024007.5(EBF1):​c.1125+4999C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0431 in 152,146 control chromosomes in the GnomAD database, including 575 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 0.043 (575 hom., cov: 33)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 0 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024007.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBF1	NM_024007.5	MANE Select	c.1125+4999C>T		intron	N/A	NP_076870.1
	EBF1	NM_001324101.2		c.1128+4999C>T		intron	N/A	NP_001311030.1
	EBF1	NM_001324103.2		c.1125+4999C>T		intron	N/A	NP_001311032.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBF1	ENST00000313708.11	TSL:1 MANE Select	c.1125+4999C>T		intron	N/A	ENSP00000322898.6
	EBF1	ENST00000380654.8	TSL:1	c.1032+4999C>T		intron	N/A	ENSP00000370029.4
	EBF1	ENST00000517373.1	TSL:5	c.1101+4999C>T		intron	N/A	ENSP00000428020.1

Frequencies

GnomAD3 genomes AF: 0.0431 AC: 6550 AN: 152028 Hom.: 575 Cov.: 33

Gnomad AFR AF: 0.0251

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.0817

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00560

Gnomad OTH AF: 0.0384

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

GnomAD4 genome AF: 0.0431 AC: 6554 AN: 152146 Hom.: 575 Cov.: 33 AF XY: 0.0509 AC XY: 3783 AN XY: 74370

African (AFR) AF: 0.0251 AC: 1044 AN: 41512

American (AMR) AF: 0.173 AC: 2651 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00750 AC: 26 AN: 3468

East Asian (EAS) AF: 0.231 AC: 1197 AN: 5180

South Asian (SAS) AF: 0.0820 AC: 395 AN: 4818

European-Finnish (FIN) AF: 0.0736 AC: 777 AN: 10556

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00560 AC: 381 AN: 68018

Other (OTH) AF: 0.0370 AC: 78 AN: 2108

Alfa AF: 0.00996 Hom.: 14

Bravo AF: 0.0551

Asia WGS AF: 0.139 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	12
DANN	Benign	0.85
PhyloP100		1.1
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: rs17056131; hg19: chr5-158153078;