8-25861178-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_022659.4(EBF2):c.1213G>A(p.Val405Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00007 in 1,613,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022659.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EBF2 | ENST00000520164.6 | c.1213G>A | p.Val405Ile | missense_variant | Exon 13 of 16 | 2 | NM_022659.4 | ENSP00000430241.1 | ||
EBF2 | ENST00000408929.7 | c.769G>A | p.Val257Ile | missense_variant | Exon 12 of 15 | 2 | ENSP00000386178.3 | |||
EBF2 | ENST00000535548.1 | c.406G>A | p.Val136Ile | missense_variant | Exon 5 of 9 | 2 | ENSP00000437909.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000562 AC: 14AN: 248994Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135078
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461654Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727124
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1213G>A (p.V405I) alteration is located in exon 13 (coding exon 13) of the EBF2 gene. This alteration results from a G to A substitution at nucleotide position 1213, causing the valine (V) at amino acid position 405 to be replaced by an isoleucine (I). 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