dbSNP rs286891: EHF:p.Ile275Ile (chr11-34658853-T-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_012153.6(EHF):c.825T>A(p.Ile275Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,612,116 control chromosomes in the GnomAD database, including 11,556 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 0.10 ( 953 hom., cov: 32)

Exomes 𝑓: 0.11 ( 10603 hom. )

Consequence

EHF
NM_012153.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0480

Publications

15 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP7

Synonymous conserved (PhyloP=0.048 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EHF	NM_012153.6 link	c.825T>A	p.Ile275Ile	synonymous_variant	Exon 9 of 9	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.825T>A	p.Ile275Ile	synonymous_variant	Exon 9 of 9	1	NM_012153.6	ENSP00000257831.3		Q9NZC4-1

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15728

AN:

152024

Hom.:

956

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0611

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.0953

Gnomad ASJ

AF:

0.0651

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.0918

GnomAD2 exomes

AF:

0.123

AC:

30690

AN:

249672

AF XY:

0.130

show subpopulations

Gnomad AFR exome

AF:

0.0612

Gnomad AMR exome

AF:

0.0679

Gnomad ASJ exome

AF:

0.0669

Gnomad EAS exome

AF:

0.131

Gnomad FIN exome

AF:

0.184

Gnomad NFE exome

AF:

0.109

Gnomad OTH exome

AF:

0.116

GnomAD4 exome

AF:

0.113

AC:

164775

AN:

1459974

Hom.:

10603

Cov.:

AF XY:

0.117

AC XY:

85145

AN XY:

726230

show subpopulations

African (AFR)

AF:

0.0557

AC:

1859

AN:

33356

American (AMR)

AF:

0.0701

AC:

3117

AN:

44478

Ashkenazi Jewish (ASJ)

AF:

0.0645

AC:

1682

AN:

26086

East Asian (EAS)

AF:

0.112

AC:

4454

AN:

39652

South Asian (SAS)

AF:

0.240

AC:

20626

AN:

85840

European-Finnish (FIN)

AF:

0.182

AC:

9691

AN:

53388

Middle Eastern (MID)

AF:

0.0942

AC:

543

AN:

5762

European-Non Finnish (NFE)

AF:

0.105

AC:

116163

AN:

1111090

Other (OTH)

AF:

0.110

AC:

6640

AN:

60322

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

6784

13569

20353

27138

33922

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4342

8684

13026

17368

21710

<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:

0.103

AC:

15725

AN:

152142

Hom.:

953

Cov.:

AF XY:

0.109

AC XY:

8123

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.0610

AC:

2533

AN:

41530

American (AMR)

AF:

0.0953

AC:

1455

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.0651

AC:

226

AN:

3470

East Asian (EAS)

AF:

0.134

AC:

692

AN:

5180

South Asian (SAS)

AF:

0.251

AC:

1208

AN:

4816

European-Finnish (FIN)

AF:

0.193

AC:

2041

AN:

10574

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.107

AC:

7290

AN:

67992

Other (OTH)

AF:

0.0899

AC:

190

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

730

1460

2191

2921

3651

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<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:

0.0979

Hom.:

249

Bravo

AF:

0.0890

Asia WGS

AF:

0.183

AC:

637

AN:

3478

EpiCase

AF:

0.0994

EpiControl

AF:

0.107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

7.5

(source)

DANN

Benign

0.70

PhyloP100

0.048

Mutation Taster

=94/6

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