rs4987414
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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. 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
NM_012153.6 intron
Scores
Not classified
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]
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ACMG classification
Classification made for transcript
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: 44700AN: 151812Hom.: 6768 Cov.: 18
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GnomAD3 exomes AF: 0.327 AC: 81309AN: 248426Hom.: 14183 AF XY: 0.330 AC XY: 44347AN XY: 134462
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GnomAD4 exome AF: 0.302 AC: 428205AN: 1417524Hom.: 67274 Cov.: 0 AF XY: 0.306 AC XY: 216714AN XY: 708058
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GnomAD4 genome ? AF: 0.294 AC: 44725AN: 151930Hom.: 6767 Cov.: 18 AF XY: 0.298 AC XY: 22137AN XY: 74244
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ClinVar
Not reported inComputational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at