chr18-5397140-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012307.5(EPB41L3):c.2759C>A(p.Ala920Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000168 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. A920V) 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>A | p.Ala920Asp | missense_variant | 18/23 | ENST00000341928.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L3 | ENST00000341928.7 | c.2759C>A | p.Ala920Asp | missense_variant | 18/23 | 1 | NM_012307.5 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251360Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135828
GnomAD4 exome AF: 0.000169 AC: 247AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.000166 AC XY: 121AN XY: 727218
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2022 | The c.2759C>A (p.A920D) alteration is located in exon 18 (coding exon 17) of the EPB41L3 gene. This alteration results from a C to A substitution at nucleotide position 2759, causing the alanine (A) at amino acid position 920 to be replaced by an aspartic acid (D). 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