1-155063931-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The ENST00000368409.8(EFNA4):c.108C>A(p.Asn36Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000713 in 1,403,430 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000368409.8 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFNA4 | NM_005227.3 | c.108C>A | p.Asn36Lys | missense_variant | 1/4 | ENST00000368409.8 | NP_005218.1 | |
EFNA4-EFNA3 | NM_001407761.1 | c.108C>A | p.Asn36Lys | missense_variant | 1/5 | NP_001394690.1 | ||
DCST1-AS1 | NR_040773.1 | n.61G>T | non_coding_transcript_exon_variant | 1/4 | ||||
ADAM15-EFNA4 | NR_176418.1 | n.3426C>A | non_coding_transcript_exon_variant | 22/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EFNA4 | ENST00000368409.8 | c.108C>A | p.Asn36Lys | missense_variant | 1/4 | 1 | NM_005227.3 | ENSP00000357394 | ||
EFNA4 | ENST00000359751.8 | c.108C>A | p.Asn36Lys | missense_variant | 1/4 | 1 | ENSP00000352789 | P2 | ||
EFNA4 | ENST00000427683.2 | c.108C>A | p.Asn36Lys | missense_variant | 1/4 | 2 | ENSP00000414378 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 7.13e-7 AC: 1AN: 1403430Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 694974
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 12, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with EFNA4-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 36 of the EFNA4 protein (p.Asn36Lys). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.