2-73292049-G-A
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001965.4(EGR4):c.869C>T(p.Pro290Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000627 in 1,609,384 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001965.4 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGR4 | ENST00000436467.4 | c.869C>T | p.Pro290Leu | missense_variant | Exon 2 of 2 | 1 | NM_001965.4 | ENSP00000419687.1 | ||
EGR4 | ENST00000545030.1 | c.1178C>T | p.Pro393Leu | missense_variant | Exon 2 of 2 | 1 | ENSP00000445626.1 | |||
ENSG00000310032 | ENST00000846694.1 | n.174-6517G>A | intron_variant | Intron 1 of 4 |
Frequencies
GnomAD3 genomes AF: 0.000467 AC: 71AN: 152170Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000587 AC: 140AN: 238316 AF XY: 0.000513 show subpopulations
GnomAD4 exome AF: 0.000644 AC: 938AN: 1457096Hom.: 0 Cov.: 31 AF XY: 0.000585 AC XY: 424AN XY: 724512 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000466 AC: 71AN: 152288Hom.: 0 Cov.: 33 AF XY: 0.000483 AC XY: 36AN XY: 74458 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at