rs2229294
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001965.4(EGR4):c.*52C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,527,060 control chromosomes in the GnomAD database, including 15,401 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 0.18 ( 3886 hom., cov: 33)
Exomes 𝑓: 0.094 ( 11515 hom. )
Consequence
EGR4
NM_001965.4 3_prime_UTR
NM_001965.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.623
Genes affected
EGR4 (HGNC:3241): (early growth response 4) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EGR4 | NM_001965.4 | c.*52C>T | 3_prime_UTR_variant | 2/2 | ENST00000436467.4 | ||
EGR4 | XM_047443603.1 | c.*52C>T | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGR4 | ENST00000436467.4 | c.*52C>T | 3_prime_UTR_variant | 2/2 | 1 | NM_001965.4 | P2 | ||
EGR4 | ENST00000545030.1 | c.*52C>T | 3_prime_UTR_variant | 2/2 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.176 AC: 26737AN: 152098Hom.: 3873 Cov.: 33
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GnomAD4 exome AF: 0.0944 AC: 129848AN: 1374842Hom.: 11515 Cov.: 31 AF XY: 0.0963 AC XY: 64975AN XY: 674382
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GnomAD4 genome ? AF: 0.176 AC: 26789AN: 152218Hom.: 3886 Cov.: 33 AF XY: 0.178 AC XY: 13223AN XY: 74416
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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