rs286925

chr11-34621121-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
EHF	NM_012153.6	c.-111A>G		5_prime_UTR_variant	1/9	ENST00000257831.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EHF	ENST00000257831.8	c.-111A>G		5_prime_UTR_variant	1/9	1	NM_012153.6	P1
EHF	ENST00000527001.5	n.29A>G		non_coding_transcript_exon_variant	1/4	4
EHF	ENST00000450654.6			upstream_gene_variant		1

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

Gnomad4 NFE exome AF: 1.00

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

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.724

Alfa AF: 0.789 Hom.: 63704

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

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

LitVar

Other links and lift over

dbSNP: rs286925; hg19: chr11-34642668;