ENST00000907181.1:c.-4+802T>C

Variant names:

• chr11-34617953-T-C
• rs286928
• ENST00000907181.1:c.-4+802T>C

Variant summary

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

The ENST00000907181.1(EHF):​c.-4+802T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.948 in 152,342 control chromosomes in the GnomAD database, including 68,551 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 0.95 (68551 hom., cov: 33)
• Consequence: EHF ENST00000907181.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 3 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=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000907181.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EHF	ENST00000907181.1		c.-4+802T>C		intron	N/A	ENSP00000577240.1
	EHF	ENST00000951052.1		c.-4+802T>C		intron	N/A	ENSP00000621111.1

Frequencies

GnomAD3 genomes AF: 0.948 AC: 144332 AN: 152224 Hom.: 68489 Cov.: 33

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.948 AC: 144454 AN: 152342 Hom.: 68551 Cov.: 33 AF XY: 0.949 AC XY: 70693 AN XY: 74498

African (AFR) AF: 0.952 AC: 39584 AN: 41570

American (AMR) AF: 0.951 AC: 14558 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3292 AN: 3472

East Asian (EAS) AF: 0.924 AC: 4786 AN: 5178

South Asian (SAS) AF: 0.867 AC: 4189 AN: 4830

European-Finnish (FIN) AF: 0.984 AC: 10458 AN: 10626

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64471 AN: 68042

Other (OTH) AF: 0.936 AC: 1980 AN: 2116

Alfa AF: 0.946 Hom.: 17924

Bravo AF: 0.948

Asia WGS AF: 0.880 AC: 3063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.1
DANN	Benign	0.45
PhyloP100		0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs286928; hg19: chr11-34639500;