1-155066990-T-C
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4BS2
The NM_182689.2(EFNA4):c.374T>C(p.Leu125Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,460,284 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182689.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -3 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_182689.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| EFNA4 | NM_005227.3 | MANE Select | c.374T>C | p.Leu125Ser | missense | Exon 2 of 4 | NP_005218.1 | ||
| EFNA4 | NM_182689.2 | c.374T>C | p.Leu125Ser | missense | Exon 2 of 4 | NP_872631.1 | |||
| EFNA4 | NM_182690.3 | c.374T>C | p.Leu125Ser | missense | Exon 2 of 4 | NP_872632.2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| EFNA4 | ENST00000368409.8 | TSL:1 MANE Select | c.374T>C | p.Leu125Ser | missense | Exon 2 of 4 | ENSP00000357394.3 | ||
| EFNA4 | ENST00000359751.8 | TSL:1 | c.374T>C | p.Leu125Ser | missense | Exon 2 of 4 | ENSP00000352789.4 | ||
| EFNA4-EFNA3 | ENST00000505139.1 | TSL:2 | c.113+3054T>C | intron | N/A | ENSP00000426741.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460284Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726376 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 32
ClinVar
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at