chr5-158713065-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_024007.5(EBF1):c.1274C>T(p.Ala425Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,599,370 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_024007.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EBF1 | NM_024007.5 | c.1274C>T | p.Ala425Val | missense_variant | 13/16 | ENST00000313708.11 | NP_076870.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EBF1 | ENST00000313708.11 | c.1274C>T | p.Ala425Val | missense_variant | 13/16 | 1 | NM_024007.5 | ENSP00000322898 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152122Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000553 AC: 8AN: 1447248Hom.: 0 Cov.: 31 AF XY: 0.00000278 AC XY: 2AN XY: 719456
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2023 | The c.1274C>T (p.A425V) alteration is located in exon 13 (coding exon 13) of the EBF1 gene. This alteration results from a C to T substitution at nucleotide position 1274, causing the alanine (A) at amino acid position 425 to be replaced by a valine (V). 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