dbSNP rs3818514: EHF:c.608-27G>A (chr11-34658506-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_012153.6(EHF):c.608-27G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 1,596,852 control chromosomes in the GnomAD database, including 201,123 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. There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.41 ( 14523 hom., cov: 31)

Exomes 𝑓: 0.50 ( 186600 hom. )

Consequence

EHF
NM_012153.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.13

Publications

9 publications found

Variant links:

Genes affected

EHF (HGNC:3246): (ETS homologous factor) This gene encodes a protein that belongs to an ETS transcription factor subfamily characterized by epithelial-specific expression (ESEs). The encoded protein acts as a transcriptional repressor and may be involved in epithelial differentiation and carcinogenesis. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2011]

EHF links:

ENSG00000309708 (HGNC:):

ENSG00000309708 links:

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ACMG classification

Classification was made for transcript

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

BP4

This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 0 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EHF	NM_012153.6 link	c.608-27G>A		intron_variant	Intron 7 of 8	ENST00000257831.8	NP_036285.2	Q9NZC4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EHF	ENST00000257831.8 link	c.608-27G>A		intron_variant	Intron 7 of 8	1	NM_012153.6	ENSP00000257831.3		Q9NZC4-1

Frequencies

GnomAD3 genomes

AF:

0.412

AC:

62585

AN:

151784

Hom.:

14518

Cov.:

show subpopulations

Gnomad AFR

AF:

0.237

Gnomad AMI

AF:

0.757

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.539

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.419

Gnomad FIN

AF:

0.463

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.453

GnomAD2 exomes

AF:

0.423

AC:

103441

AN:

244430

AF XY:

0.438

show subpopulations

Gnomad AFR exome

AF:

0.234

Gnomad AMR exome

AF:

0.241

Gnomad ASJ exome

AF:

0.542

Gnomad EAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.469

Gnomad NFE exome

AF:

0.532

Gnomad OTH exome

AF:

0.460

GnomAD4 exome

AF:

0.498

AC:

720098

AN:

1444950

Hom.:

186600

Cov.:

AF XY:

0.499

AC XY:

358310

AN XY:

717714

show subpopulations

African (AFR)

AF:

0.222

AC:

7302

AN:

32830

American (AMR)

AF:

0.253

AC:

11059

AN:

43688

Ashkenazi Jewish (ASJ)

AF:

0.550

AC:

14085

AN:

25612

East Asian (EAS)

AF:

0.143

AC:

5644

AN:

39494

South Asian (SAS)

AF:

0.441

AC:

37291

AN:

84494

European-Finnish (FIN)

AF:

0.469

AC:

24826

AN:

52956

Middle Eastern (MID)

AF:

0.539

AC:

3062

AN:

5676

European-Non Finnish (NFE)

AF:

0.535

AC:

588447

AN:

1100538

Other (OTH)

AF:

0.476

AC:

28382

AN:

59662

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

17438

34876

52313

69751

87189

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.412

AC:

62599

AN:

151902

Hom.:

14523

Cov.:

AF XY:

0.407

AC XY:

30214

AN XY:

74222

show subpopulations

African (AFR)

AF:

0.237

AC:

9805

AN:

41438

American (AMR)

AF:

0.351

AC:

5364

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.539

AC:

1866

AN:

3464

East Asian (EAS)

AF:

0.129

AC:

668

AN:

5164

South Asian (SAS)

AF:

0.420

AC:

2013

AN:

4798

European-Finnish (FIN)

AF:

0.463

AC:

4879

AN:

10530

Middle Eastern (MID)

AF:

0.439

AC:

129

AN:

294

European-Non Finnish (NFE)

AF:

0.534

AC:

36243

AN:

67934

Other (OTH)

AF:

0.448

AC:

942

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1723

3446

5170

6893

8616

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.493

Hom.:

76399

Bravo

AF:

0.391

Asia WGS

AF:

0.223

AC:

777

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.020

(source)

DANN

Benign

0.63

PhyloP100

-2.1

BranchPoint Hunter

0.0

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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rs3818514

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