dbSNP rs6895454: EBF1:c.355+184G>A (chr5-159096159-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024007.5(EBF1):c.355+184G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 636,854 control chromosomes in the GnomAD database, including 6,276 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 0.14 ( 1950 hom., cov: 33)

Exomes 𝑓: 0.11 ( 4326 hom. )

Consequence

EBF1
NM_024007.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0280

Publications

9 publications found

Variant links:

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]

EBF1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EBF1	NM_024007.5	MANE Select	c.355+184G>A	intron	N/A	NP_076870.1	Q9UH73-1
EBF1	NM_001324101.2		c.355+184G>A	intron	N/A	NP_001311030.1
EBF1	NM_001324103.2		c.355+184G>A	intron	N/A	NP_001311032.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EBF1	ENST00000313708.11	TSL:1 MANE Select	c.355+184G>A	intron	N/A	ENSP00000322898.6	Q9UH73-1
EBF1	ENST00000380654.8	TSL:1	c.355+184G>A	intron	N/A	ENSP00000370029.4	Q9UH73-2
EBF1	ENST00000964682.1		c.355+184G>A	intron	N/A	ENSP00000634741.1

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20760

AN:

152064

Hom.:

1954

Cov.:

show subpopulations

Gnomad AFR

AF:

0.238

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.0842

Gnomad EAS

AF:

0.393

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.0766

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0749

Gnomad OTH

AF:

0.122

GnomAD4 exome

AF:

0.106

AC:

51203

AN:

484672

Hom.:

4326

AF XY:

0.104

AC XY:

26483

AN XY:

254482

show subpopulations

African (AFR)

AF:

0.233

AC:

3015

AN:

12920

American (AMR)

AF:

0.145

AC:

2674

AN:

18484

Ashkenazi Jewish (ASJ)

AF:

0.0845

AC:

1172

AN:

13872

East Asian (EAS)

AF:

0.375

AC:

11669

AN:

31076

South Asian (SAS)

AF:

0.100

AC:

4606

AN:

45962

European-Finnish (FIN)

AF:

0.0796

AC:

2386

AN:

29974

Middle Eastern (MID)

AF:

0.0887

AC:

183

AN:

2064

European-Non Finnish (NFE)

AF:

0.0743

AC:

22532

AN:

303220

Other (OTH)

AF:

0.109

AC:

2966

AN:

27100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

2036

4072

6109

8145

10181

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

366

732

1098

1464

1830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.137

AC:

20780

AN:

152182

Hom.:

1950

Cov.:

AF XY:

0.137

AC XY:

10211

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.237

AC:

9845

AN:

41468

American (AMR)

AF:

0.122

AC:

1866

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0842

AC:

292

AN:

3468

East Asian (EAS)

AF:

0.392

AC:

2019

AN:

5152

South Asian (SAS)

AF:

0.112

AC:

541

AN:

4826

European-Finnish (FIN)

AF:

0.0766

AC:

813

AN:

10610

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0749

AC:

5095

AN:

68030

Other (OTH)

AF:

0.121

AC:

256

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

905

1809

2714

3618

4523

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.109

Hom.:

1949

Bravo

AF:

0.150

Asia WGS

AF:

0.198

AC:

688

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

6.2

(source)

DANN

Benign

0.81

PhyloP100

0.028

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over