NM_012153.6:c.-3-6954C>T

Variant names:

• chr11-34635674-C-T
• rs286911
• NM_012153.6:c.-3-6954C>T

Variant summary

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

The NM_012153.6(EHF):​c.-3-6954C>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
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 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.-3-6954C>T		intron	N/A	NP_036285.2
	EHF	NM_001206616.2		c.63+3022C>T		intron	N/A	NP_001193545.1	Q9NZC4-3
	EHF	NM_001378052.1		c.63+3022C>T		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.-3-6954C>T		intron	N/A	ENSP00000257831.3	Q9NZC4-1
	EHF	ENST00000531794.5	TSL:1	c.63+3022C>T		intron	N/A	ENSP00000435835.1	Q9NZC4-3
	EHF	ENST00000530286.5	TSL:1	c.-3-6954C>T		intron	N/A	ENSP00000433508.1	Q9NZC4-1

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

African (AFR) AF: 0.515 AC: 20633 AN: 40026

American (AMR) AF: 0.483 AC: 7140 AN: 14794

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1451 AN: 3452

East Asian (EAS) AF: 0.295 AC: 1478 AN: 5016

South Asian (SAS) AF: 0.256 AC: 1193 AN: 4656

European-Finnish (FIN) AF: 0.268 AC: 2392 AN: 8912

Middle Eastern (MID) AF: 0.387 AC: 110 AN: 284

European-Non Finnish (NFE) AF: 0.323 AC: 21783 AN: 67366

Other (OTH) AF: 0.385 AC: 788 AN: 2048

Alfa AF: 0.342 Hom.: 6224

Bravo AF: 0.406

Asia WGS AF: 0.290 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.66
PhyloP100		0.016
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: rs286911; hg19: chr11-34657221;