chr18-5397129-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_012307.5(EPB41L3):c.2770C>T(p.Arg924Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00116 in 1,614,114 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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.2770C>T | p.Arg924Cys | missense_variant | 18/23 | ENST00000341928.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L3 | ENST00000341928.7 | c.2770C>T | p.Arg924Cys | missense_variant | 18/23 | 1 | NM_012307.5 |
Frequencies
GnomAD3 genomes ? AF: 0.00597 AC: 909AN: 152204Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00168 AC: 422AN: 251310Hom.: 6 AF XY: 0.00132 AC XY: 179AN XY: 135784
GnomAD4 exome AF: 0.000663 AC: 969AN: 1461792Hom.: 8 Cov.: 31 AF XY: 0.000628 AC XY: 457AN XY: 727194
GnomAD4 genome ? AF: 0.00597 AC: 909AN: 152322Hom.: 9 Cov.: 32 AF XY: 0.00575 AC XY: 428AN XY: 74478
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