18-5397140-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012307.5(EPB41L3):c.2759C>T(p.Ala920Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000297 in 1,614,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A920D) has been classified as Uncertain significance.
Frequency
Consequence
NM_012307.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPB41L3 | NM_012307.5 | c.2759C>T | p.Ala920Val | missense_variant | 18/23 | ENST00000341928.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L3 | ENST00000341928.7 | c.2759C>T | p.Ala920Val | missense_variant | 18/23 | 1 | NM_012307.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251360Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135828
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727218
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 28, 2021 | The c.2759C>T (p.A920V) alteration is located in exon 18 (coding exon 17) of the EPB41L3 gene. This alteration results from a C to T substitution at nucleotide position 2759, causing the alanine (A) at amino acid position 920 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at