chr1-225886991-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_020997.4(LEFTY1):c.837G>T(p.Glu279Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000000686 in 1,457,684 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E279K) has been classified as Benign.
Frequency
Consequence
NM_020997.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LEFTY1 | NM_020997.4 | c.837G>T | p.Glu279Asp | missense_variant | 4/4 | ENST00000272134.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LEFTY1 | ENST00000272134.5 | c.837G>T | p.Glu279Asp | missense_variant | 4/4 | 1 | NM_020997.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457684Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 724518
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at