chrX-48523848-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP4_ModerateBS2
The NM_006579.3(EBP):c.77G>A(p.Arg26His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000613 in 1,207,326 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006579.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EBP | NM_006579.3 | c.77G>A | p.Arg26His | missense_variant | 2/5 | ENST00000495186.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EBP | ENST00000495186.6 | c.77G>A | p.Arg26His | missense_variant | 2/5 | 1 | NM_006579.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000366 AC: 4AN: 109204Hom.: 0 Cov.: 21 AF XY: 0.0000315 AC XY: 1AN XY: 31716
GnomAD3 exomes AF: 0.0000709 AC: 13AN: 183334Hom.: 0 AF XY: 0.0000738 AC XY: 5AN XY: 67774
GnomAD4 exome AF: 0.0000637 AC: 70AN: 1098122Hom.: 0 Cov.: 34 AF XY: 0.0000468 AC XY: 17AN XY: 363476
GnomAD4 genome ? AF: 0.0000366 AC: 4AN: 109204Hom.: 0 Cov.: 21 AF XY: 0.0000315 AC XY: 1AN XY: 31716
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 26, 2023 | This variant has not been reported in the literature in individuals affected with EBP-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 26 of the EBP protein (p.Arg26His). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The histidine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at