rs286911

chr11-34635674-C-T

Variant summary

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

The NM_012153.6(EHF):c.-3-6954C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 147,446 control chromosomes in the GnomAD database, including 11,840 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 0.39 (11840 hom., cov: 25)
• Consequence: EHF NM_012153.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

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 (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EHF	NM_012153.6	c.-3-6954C>T		intron_variant		ENST00000257831.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EHF	ENST00000257831.8	c.-3-6954C>T		intron_variant		1	NM_012153.6	P1

Frequencies

GnomAD3 genomes AF: 0.388 AC: 57149 AN: 147384 Hom.: 11826 Cov.: 25

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.374

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.388 AC: 57178 AN: 147446 Hom.: 11840 Cov.: 25 AF XY: 0.387 AC XY: 27662 AN XY: 71408

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.385

Alfa AF: 0.341 Hom.: 5655

Bravo AF: 0.406

Asia WGS AF: 0.290 AC: 1006 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	4.2
Dann	Benign	0.66

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: rs286911; hg19: chr11-34657221;