chr5-158708039-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_024007.5(EBF1):c.1684G>A(p.Val562Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,553,594 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024007.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EBF1 | NM_024007.5 | c.1684G>A | p.Val562Ile | missense_variant | 15/16 | ENST00000313708.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EBF1 | ENST00000313708.11 | c.1684G>A | p.Val562Ile | missense_variant | 15/16 | 1 | NM_024007.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000187 AC: 3AN: 160422Hom.: 0 AF XY: 0.0000118 AC XY: 1AN XY: 84460
GnomAD4 exome AF: 0.0000157 AC: 22AN: 1401334Hom.: 0 Cov.: 31 AF XY: 0.0000174 AC XY: 12AN XY: 691454
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.1684G>A (p.V562I) alteration is located in exon 15 (coding exon 15) of the EBF1 gene. This alteration results from a G to A substitution at nucleotide position 1684, causing the valine (V) at amino acid position 562 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