8-25861133-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_022659.4(EBF2):c.1258G>A(p.Ala420Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022659.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EBF2 | ENST00000520164.6 | c.1258G>A | p.Ala420Thr | missense_variant | Exon 13 of 16 | 2 | NM_022659.4 | ENSP00000430241.1 | ||
EBF2 | ENST00000408929.7 | c.814G>A | p.Ala272Thr | missense_variant | Exon 12 of 15 | 2 | ENSP00000386178.3 | |||
EBF2 | ENST00000535548.1 | c.451G>A | p.Ala151Thr | missense_variant | Exon 5 of 9 | 2 | ENSP00000437909.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249526Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135372
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727246
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1258G>A (p.A420T) 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 1258, causing the alanine (A) at amino acid position 420 to be replaced by a threonine (T). 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