2-73291713-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001965.4(EGR4):c.1205G>T(p.Arg402Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000442 in 1,605,652 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001965.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGR4 | ENST00000436467.4 | c.1205G>T | p.Arg402Leu | missense_variant | Exon 2 of 2 | 1 | NM_001965.4 | ENSP00000419687.1 | ||
EGR4 | ENST00000545030.1 | c.1514G>T | p.Arg505Leu | missense_variant | Exon 2 of 2 | 1 | ENSP00000445626.1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152018Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000165 AC: 4AN: 242828Hom.: 0 AF XY: 0.00000757 AC XY: 1AN XY: 132110
GnomAD4 exome AF: 0.0000447 AC: 65AN: 1453634Hom.: 0 Cov.: 32 AF XY: 0.0000401 AC XY: 29AN XY: 723584
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152018Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1514G>T (p.R505L) alteration is located in exon 2 (coding exon 2) of the EGR4 gene. This alteration results from a G to T substitution at nucleotide position 1514, causing the arginine (R) at amino acid position 505 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at