chr18-5397324-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_012307.5(EPB41L3):c.2575G>C(p.Glu859Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00139 in 1,614,070 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_012307.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPB41L3 | NM_012307.5 | c.2575G>C | p.Glu859Gln | missense_variant | 18/23 | ENST00000341928.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L3 | ENST00000341928.7 | c.2575G>C | p.Glu859Gln | missense_variant | 18/23 | 1 | NM_012307.5 |
Frequencies
GnomAD3 genomes ? AF: 0.00733 AC: 1115AN: 152212Hom.: 15 Cov.: 32
GnomAD3 exomes AF: 0.00187 AC: 470AN: 251152Hom.: 6 AF XY: 0.00137 AC XY: 186AN XY: 135774
GnomAD4 exome AF: 0.000777 AC: 1136AN: 1461740Hom.: 14 Cov.: 31 AF XY: 0.000690 AC XY: 502AN XY: 727198
GnomAD4 genome ? AF: 0.00730 AC: 1112AN: 152330Hom.: 15 Cov.: 32 AF XY: 0.00752 AC XY: 560AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at