chr10-129840260-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_001375380.1(EBF3):c.1744G>A(p.Gly582Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000443 in 1,579,232 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001375380.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EBF3 | NM_001375380.1 | c.1744G>A | p.Gly582Arg | missense_variant | Exon 15 of 17 | ENST00000440978.2 | NP_001362309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EBF3 | ENST00000440978.2 | c.1744G>A | p.Gly582Arg | missense_variant | Exon 15 of 17 | 3 | NM_001375380.1 | ENSP00000387543.2 | ||
EBF3 | ENST00000368648.8 | c.1609G>A | p.Gly537Arg | missense_variant | Exon 16 of 17 | 1 | ENSP00000357637.3 | |||
EBF3 | ENST00000355311.10 | c.1744G>A | p.Gly582Arg | missense_variant | Exon 15 of 16 | 5 | ENSP00000347463.4 | |||
EBF3 | ENST00000675373.1 | n.1281G>A | non_coding_transcript_exon_variant | Exon 12 of 14 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000350 AC: 5AN: 1426996Hom.: 0 Cov.: 37 AF XY: 0.00000708 AC XY: 5AN XY: 706236
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74372
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1609G>A (p.G537R) alteration is located in exon 15 (coding exon 15) of the EBF3 gene. This alteration results from a G to A substitution at nucleotide position 1609, causing the glycine (G) at amino acid position 537 to be replaced by an arginine (R). 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