chrX-48523830-A-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM1BP4_ModerateBP6BS2
The NM_006579.3(EBP):c.59A>C(p.Asn20Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000212 in 1,207,001 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 78 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006579.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EBP | NM_006579.3 | c.59A>C | p.Asn20Thr | missense_variant | 2/5 | ENST00000495186.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EBP | ENST00000495186.6 | c.59A>C | p.Asn20Thr | missense_variant | 2/5 | 1 | NM_006579.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000184 AC: 2AN: 108858Hom.: 0 Cov.: 21 AF XY: 0.0000320 AC XY: 1AN XY: 31242
GnomAD3 exomes AF: 0.0000492 AC: 9AN: 182836Hom.: 0 AF XY: 0.0000743 AC XY: 5AN XY: 67312
GnomAD4 exome AF: 0.000231 AC: 254AN: 1098143Hom.: 0 Cov.: 34 AF XY: 0.000212 AC XY: 77AN XY: 363501
GnomAD4 genome ? AF: 0.0000184 AC: 2AN: 108858Hom.: 0 Cov.: 21 AF XY: 0.0000320 AC XY: 1AN XY: 31242
ClinVar
Submissions by phenotype
Connective tissue disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Mar 01, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at