rs4987414

chr11-34651504-AG-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_012153.6(EHF):c.407-37del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 1,569,454 control chromosomes in the GnomAD database, including 74,041 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.29 (6767 hom., cov: 18)
  • Exomes 𝑓: 0.30 (67274 hom.)
• Consequence: EHF NM_012153.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EHF	NM_012153.6	c.407-37del		intron_variant		ENST00000257831.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EHF	ENST00000257831.8	c.407-37del		intron_variant		1	NM_012153.6	P1

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44700 AN: 151812 Hom.: 6768 Cov.: 18

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.285

GnomAD3 exomes AF: 0.327 AC: 81309 AN: 248426 Hom.: 14183 AF XY: 0.330 AC XY: 44347 AN XY: 134462

Gnomad AFR exome AF: 0.258

Gnomad AMR exome AF: 0.335

Gnomad ASJ exome AF: 0.245

Gnomad EAS exome AF: 0.541

Gnomad SAS exome AF: 0.440

Gnomad FIN exome AF: 0.309

Gnomad NFE exome AF: 0.281

Gnomad OTH exome AF: 0.313

GnomAD4 exome AF: 0.302 AC: 428205 AN: 1417524 Hom.: 67274 Cov.: 0 AF XY: 0.306 AC XY: 216714 AN XY: 708058

Gnomad4 AFR exome AF: 0.255

Gnomad4 AMR exome AF: 0.339

Gnomad4 ASJ exome AF: 0.242

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.436

Gnomad4 FIN exome AF: 0.312

Gnomad4 NFE exome AF: 0.285

Gnomad4 OTH exome AF: 0.306

GnomAD4 genome AF: 0.294 AC: 44725 AN: 151930 Hom.: 6767 Cov.: 18 AF XY: 0.298 AC XY: 22137 AN XY: 74244

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.284

Alfa AF: 0.152 Hom.: 591

Bravo AF: 0.292

Asia WGS AF: 0.452 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs4987414; hg19: chr11-34673051; COSMIC: COSV57667410; COSMIC: COSV57667410;