chr11-34633816-A-G

Variant names:

• chr11-34633816-A-G
• rs286913
• NM_012153.6:c.-3-8812A>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.-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
• Publications: 16 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=-0.63).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012153.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EHF	NM_012153.6	MANE Select	c.-3-8812A>G		intron	N/A	NP_036285.2
	EHF	NM_001206616.2		c.63+1164A>G		intron	N/A	NP_001193545.1	Q9NZC4-3
	EHF	NM_001378052.1		c.63+1164A>G		intron	N/A	NP_001364981.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EHF	ENST00000257831.8	TSL:1 MANE Select	c.-3-8812A>G		intron	N/A	ENSP00000257831.3	Q9NZC4-1
	EHF	ENST00000531794.5	TSL:1	c.63+1164A>G		intron	N/A	ENSP00000435835.1	Q9NZC4-3
	EHF	ENST00000530286.5	TSL:1	c.-3-8812A>G		intron	N/A	ENSP00000433508.1	Q9NZC4-1

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

African (AFR) AF: 0.931 AC: 38664 AN: 41512

American (AMR) AF: 0.948 AC: 14504 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.947 AC: 3289 AN: 3472

East Asian (EAS) AF: 0.926 AC: 4790 AN: 5170

South Asian (SAS) AF: 0.872 AC: 4196 AN: 4814

European-Finnish (FIN) AF: 0.984 AC: 10452 AN: 10624

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64444 AN: 68020

Other (OTH) AF: 0.926 AC: 1951 AN: 2106

Alfa AF: 0.944 Hom.: 284274

Bravo AF: 0.941

Asia WGS AF: 0.877 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	18
DANN	Benign	0.74
PhyloP100		0.28
Mutation Taster		=100/0	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: rs286913; hg19: chr11-34655363;