11-34641414-A-G

Position:

• chr11-34641414-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.-3-1214A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,132 control chromosomes in the GnomAD database, including 49,000 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 0.80 (49000 hom., cov: 32)
• Consequence: EHF NM_012153.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EHF	NM_012153.6	c.-3-1214A>G		intron_variant		ENST00000257831.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EHF	ENST00000257831.8	c.-3-1214A>G		intron_variant		1	NM_012153.6	P1

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121493 AN: 152012 Hom.: 48970 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.826

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.799 AC: 121570 AN: 152132 Hom.: 49000 Cov.: 32 AF XY: 0.797 AC XY: 59250 AN XY: 74362

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.819

Alfa AF: 0.850 Hom.: 73017

Bravo AF: 0.788

Asia WGS AF: 0.730 AC: 2543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.21

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: rs286905; hg19: chr11-34662961;