chrX-48523786-G-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_006579.3(EBP):c.15G>T(p.Ala5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 1,195,442 control chromosomes in the GnomAD database, including 47,684 homozygotes. There are 128,731 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A5A) has been classified as Likely benign.
Frequency
Consequence
NM_006579.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EBP | NM_006579.3 | c.15G>T | p.Ala5= | synonymous_variant | 2/5 | ENST00000495186.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EBP | ENST00000495186.6 | c.15G>T | p.Ala5= | synonymous_variant | 2/5 | 1 | NM_006579.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.291 AC: 29826AN: 102490Hom.: 3798 Cov.: 19 AF XY: 0.263 AC XY: 6832AN XY: 26020
GnomAD3 exomes AF: 0.330 AC: 56135AN: 170094Hom.: 6532 AF XY: 0.325 AC XY: 18447AN XY: 56688
GnomAD4 exome AF: 0.341 AC: 373162AN: 1092919Hom.: 43880 Cov.: 36 AF XY: 0.339 AC XY: 121898AN XY: 359315
GnomAD4 genome ? AF: 0.291 AC: 29837AN: 102523Hom.: 3804 Cov.: 19 AF XY: 0.262 AC XY: 6833AN XY: 26065
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 29, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Chondrodysplasia punctata 2 X-linked dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
MEND syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at