chrX-48523786-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_006579.3(EBP):c.15G>A(p.Ala5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,195,834 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A5A) has been classified as Benign.
Frequency
Consequence
NM_006579.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EBP | NM_006579.3 | c.15G>A | 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>A | p.Ala5= | synonymous_variant | 2/5 | 1 | NM_006579.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000195 AC: 2AN: 102586Hom.: 0 Cov.: 19 AF XY: 0.0000384 AC XY: 1AN XY: 26030
GnomAD3 exomes AF: 0.0000176 AC: 3AN: 170094Hom.: 0 AF XY: 0.0000176 AC XY: 1AN XY: 56688
GnomAD4 exome AF: 0.0000101 AC: 11AN: 1093215Hom.: 0 Cov.: 36 AF XY: 0.0000111 AC XY: 4AN XY: 359469
GnomAD4 genome AF: 0.0000195 AC: 2AN: 102619Hom.: 0 Cov.: 19 AF XY: 0.0000384 AC XY: 1AN XY: 26075
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 13, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at