5-159075720-T-C

Variant names:

• chr5-159075720-T-C
• rs6865969
• NM_024007.5:c.486-2256A>G

Variant summary

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

The NM_024007.5(EBF1):​c.486-2256A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,064 control chromosomes in the GnomAD database, including 21,220 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 0.51 (21220 hom., cov: 32)
• Consequence: EBF1 NM_024007.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EBF1	NM_024007.5	c.486-2256A>G		intron_variant	Intron 5 of 15	ENST00000313708.11	NP_076870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EBF1	ENST00000313708.11	c.486-2256A>G		intron_variant	Intron 5 of 15	1	NM_024007.5	ENSP00000322898.6

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77620 AN: 151948 Hom.: 21192 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.511 AC: 77705 AN: 152064 Hom.: 21220 Cov.: 32 AF XY: 0.503 AC XY: 37413 AN XY: 74332

African (AFR) AF: 0.718 AC: 29770 AN: 41460

American (AMR) AF: 0.408 AC: 6230 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1816 AN: 3470

East Asian (EAS) AF: 0.511 AC: 2640 AN: 5162

South Asian (SAS) AF: 0.381 AC: 1832 AN: 4814

European-Finnish (FIN) AF: 0.403 AC: 4267 AN: 10584

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29552 AN: 67972

Other (OTH) AF: 0.484 AC: 1021 AN: 2108

Alfa AF: 0.426 Hom.: 7343

Bravo AF: 0.526

Asia WGS AF: 0.396 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.61
PhyloP100		-0.57
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: rs6865969; hg19: chr5-158502728; COSMIC: COSV58172154; COSMIC: COSV58172154;