rs286925

Variant names:

• chr11-34621121-A-G
• rs286925
• NM_012153.6:c.-111A>G

Variant summary

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

The NM_012153.6(EHF):​c.-111A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,192 control chromosomes in the GnomAD database, including 42,895 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 0.74 (42894 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: EHF NM_012153.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 13 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EHF	NM_012153.6	c.-111A>G		5_prime_UTR_variant	Exon 1 of 9	ENST00000257831.8	NP_036285.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EHF	ENST00000257831.8	c.-111A>G		5_prime_UTR_variant	Exon 1 of 9	1	NM_012153.6	ENSP00000257831.3
EHF	ENST00000527001.5	n.29A>G		non_coding_transcript_exon_variant	Exon 1 of 4	4
EHF	ENST00000450654.6	c.-111A>G		upstream_gene_variant		1		ENSP00000399733.2

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113129 AN: 152072 Hom.: 42876 Cov.: 33

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.728

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.744 AC: 113197 AN: 152190 Hom.: 42894 Cov.: 33 AF XY: 0.740 AC XY: 55078 AN XY: 74404

African (AFR) AF: 0.678 AC: 28122 AN: 41492

American (AMR) AF: 0.710 AC: 10870 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2704 AN: 3472

East Asian (EAS) AF: 0.412 AC: 2128 AN: 5168

South Asian (SAS) AF: 0.564 AC: 2721 AN: 4822

European-Finnish (FIN) AF: 0.827 AC: 8773 AN: 10602

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55330 AN: 68010

Other (OTH) AF: 0.724 AC: 1531 AN: 2116

Alfa AF: 0.784 Hom.: 79909

Bravo AF: 0.733

Asia WGS AF: 0.498 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		0.29
PromoterAI		-0.0057	Neutral
Mutation Taster		=300/0	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: rs286925; hg19: chr11-34642668;