NM_001375380.1:c.1737C>T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001375380.1(EBF3):c.1737C>T(p.Ser579Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000194 in 1,584,790 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001375380.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EBF3 | NM_001375380.1 | c.1737C>T | p.Ser579Ser | synonymous_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.1737C>T | p.Ser579Ser | synonymous_variant | Exon 15 of 17 | 3 | NM_001375380.1 | ENSP00000387543.2 | ||
EBF3 | ENST00000368648.8 | c.1602C>T | p.Ser534Ser | synonymous_variant | Exon 16 of 17 | 1 | ENSP00000357637.3 | |||
EBF3 | ENST00000355311.10 | c.1737C>T | p.Ser579Ser | synonymous_variant | Exon 15 of 16 | 5 | ENSP00000347463.4 | |||
EBF3 | ENST00000675373.1 | n.1274C>T | non_coding_transcript_exon_variant | Exon 12 of 14 |
Frequencies
GnomAD3 genomes AF: 0.000282 AC: 43AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000653 AC: 133AN: 203666Hom.: 0 AF XY: 0.000579 AC XY: 63AN XY: 108876
GnomAD4 exome AF: 0.000185 AC: 265AN: 1432460Hom.: 1 Cov.: 37 AF XY: 0.000178 AC XY: 126AN XY: 709544
GnomAD4 genome AF: 0.000282 AC: 43AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
- -
EBF3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at