18-5397161-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012307.5(EPB41L3):c.2738T>C(p.Val913Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,614,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012307.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPB41L3 | NM_012307.5 | c.2738T>C | p.Val913Ala | missense_variant | 18/23 | ENST00000341928.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L3 | ENST00000341928.7 | c.2738T>C | p.Val913Ala | missense_variant | 18/23 | 1 | NM_012307.5 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251460Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135894
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 727240
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.2738T>C (p.V913A) alteration is located in exon 18 (coding exon 17) of the EPB41L3 gene. This alteration results from a T to C substitution at nucleotide position 2738, causing the valine (V) at amino acid position 913 to be replaced by an alanine (A). 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