chr18-5397405-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_012307.5(EPB41L3):c.2494T>G(p.Ser832Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,610,620 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
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.2494T>G | p.Ser832Ala | missense_variant | 18/23 | ENST00000341928.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L3 | ENST00000341928.7 | c.2494T>G | p.Ser832Ala | missense_variant | 18/23 | 1 | NM_012307.5 |
Frequencies
GnomAD3 genomes ? AF: 0.00554 AC: 840AN: 151750Hom.: 7 Cov.: 33
GnomAD3 exomes AF: 0.00155 AC: 386AN: 249088Hom.: 5 AF XY: 0.00125 AC XY: 168AN XY: 134596
GnomAD4 exome AF: 0.000615 AC: 897AN: 1458752Hom.: 7 Cov.: 31 AF XY: 0.000589 AC XY: 427AN XY: 725356
GnomAD4 genome ? AF: 0.00553 AC: 840AN: 151868Hom.: 7 Cov.: 33 AF XY: 0.00532 AC XY: 395AN XY: 74188
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 04, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at