19-42248577-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_006494.4(ERF):āc.1535A>Gā(p.Lys512Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000316 in 1,581,284 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K512N) has been classified as Uncertain significance.
Frequency
Consequence
NM_006494.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERF | NM_006494.4 | c.1535A>G | p.Lys512Arg | missense_variant | 4/4 | ENST00000222329.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERF | ENST00000222329.9 | c.1535A>G | p.Lys512Arg | missense_variant | 4/4 | 1 | NM_006494.4 | P1 | |
ERF | ENST00000440177.6 | c.1310A>G | p.Lys437Arg | missense_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151732Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1429552Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 708514
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151732Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74102
ClinVar
Submissions by phenotype
ERF-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 31, 2023 | The ERF c.1535A>G variant is predicted to result in the amino acid substitution p.Lys512Arg. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at