11-34633816-A-G

Variant names:

• chr11-34633816-A-G
• rs286913
• NM_012153.6:c.-3-8812A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012153.6(EHF):​c.-3-8812A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.942 in 152,216 control chromosomes in the GnomAD database, including 67,648 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 0.94 (67648 hom., cov: 30)
• Consequence: EHF NM_012153.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

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=-0.63).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EHF	NM_012153.6	c.-3-8812A>G		intron_variant	Intron 1 of 8	ENST00000257831.8	NP_036285.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EHF	ENST00000257831.8	c.-3-8812A>G		intron_variant	Intron 1 of 8	1	NM_012153.6	ENSP00000257831.3

Frequencies

GnomAD3 genomes AF: 0.942 AC: 143305 AN: 152098 Hom.: 67587 Cov.: 30

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.942 AC: 143426 AN: 152216 Hom.: 67648 Cov.: 30 AF XY: 0.943 AC XY: 70154 AN XY: 74428

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.948

Gnomad4 ASJ AF: 0.947

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.984

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.926

Alfa AF: 0.943 Hom.: 145612

Bravo AF: 0.941

Asia WGS AF: 0.877 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	18
DANN	Benign	0.74

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: rs286913; hg19: chr11-34655363;