Genetic Variant ELF4:c.*884A>G (chrX-130065837-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001421.4(ELF4):c.*884A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 171,953 control chromosomes in the GnomAD database, including 6,406 homozygotes. There are 14,902 hemizygotes in GnomAD. 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 0.32 ( 4752 hom., 10315 hem., cov: 23)

Exomes 𝑓: 0.26 ( 1654 hom. 4587 hem. )

Consequence

ELF4
NM_001421.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.908

Publications

4 publications found

Variant links:

Genes affected

ELF4 (HGNC:3319): (E74 like ETS transcription factor 4) The protein encoded by this gene is a transcriptional activator that binds and activates the promoters of the CSF2, IL3, IL8, and PRF1 genes. The encoded protein is involved in natural killer cell development and function, innate immunity, and induction of cell cycle arrest in naive CD8+ cells. Two transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Jan 2010]

ELF4 Gene-Disease associations (from GenCC):

autoinflammatory syndrome, familial, X-linked, Behcet-like 2
Inheritance: XL Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
short stature due to isolated growth hormone deficiency with X-linked hypogammaglobulinemia
Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ELF4 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELF4	NM_001421.4 link	c.*884A>G		3_prime_UTR_variant	Exon 9 of 9	ENST00000308167.10	NP_001412.1	Q99607

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELF4	ENST00000308167.10 link	c.*884A>G		3_prime_UTR_variant	Exon 9 of 9	1	NM_001421.4	ENSP00000311280.6		Q99607
ELF4	ENST00000335997.11 link	c.*884A>G		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000338608.7		Q99607

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

35795

AN:

110572

Hom.:

4754

Cov.:

show subpopulations

Gnomad AFR

AF:

0.485

Gnomad AMI

AF:

0.308

Gnomad AMR

AF:

0.399

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.252

Gnomad FIN

AF:

0.245

Gnomad MID

AF:

0.349

Gnomad NFE

AF:

0.246

Gnomad OTH

AF:

0.342

GnomAD4 exome

AF:

0.262

AC:

16048

AN:

61326

Hom.:

1654

Cov.:

AF XY:

0.260

AC XY:

4587

AN XY:

17644

show subpopulations

African (AFR)

AF:

0.496

AC:

1501

AN:

3027

American (AMR)

AF:

0.427

AC:

864

AN:

2024

Ashkenazi Jewish (ASJ)

AF:

0.220

AC:

797

AN:

3627

East Asian (EAS)

AF:

0.162

AC:

1418

AN:

8730

South Asian (SAS)

AF:

0.268

AC:

132

AN:

493

European-Finnish (FIN)

AF:

0.261

AC:

AN:

Middle Eastern (MID)

AF:

0.312

AC:

103

AN:

330

European-Non Finnish (NFE)

AF:

0.257

AC:

9701

AN:

37807

Other (OTH)

AF:

0.290

AC:

1520

AN:

5242

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

446

892

1338

1784

2230

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

160

200

<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:

0.324

AC:

35832

AN:

110627

Hom.:

4752

Cov.:

AF XY:

0.313

AC XY:

10315

AN XY:

32983

show subpopulations

African (AFR)

AF:

0.486

AC:

14766

AN:

30384

American (AMR)

AF:

0.398

AC:

4154

AN:

10428

Ashkenazi Jewish (ASJ)

AF:

0.228

AC:

599

AN:

2628

East Asian (EAS)

AF:

0.117

AC:

411

AN:

3499

South Asian (SAS)

AF:

0.251

AC:

664

AN:

2646

European-Finnish (FIN)

AF:

0.245

AC:

1454

AN:

5924

Middle Eastern (MID)

AF:

0.355

AC:

AN:

211

European-Non Finnish (NFE)

AF:

0.246

AC:

12996

AN:

52738

Other (OTH)

AF:

0.338

AC:

507

AN:

1500

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

873

1746

2620

3493

4366

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

340

680

1020

1360

1700

<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:

0.269

Hom.:

15619

Bravo

AF:

0.345

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.0

(source)

DANN

Benign

0.73

PhyloP100

-0.91

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over