11-20783740-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_006157.5(NELL1):c.245G>T(p.Arg82Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,732 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R82Q) has been classified as Likely benign.
Frequency
Consequence
NM_006157.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NELL1 | NM_006157.5 | c.245G>T | p.Arg82Leu | missense_variant | Exon 3 of 20 | ENST00000357134.10 | NP_006148.2 | |
NELL1 | NM_001288713.1 | c.329G>T | p.Arg110Leu | missense_variant | Exon 4 of 21 | NP_001275642.1 | ||
NELL1 | NM_201551.2 | c.245G>T | p.Arg82Leu | missense_variant | Exon 3 of 19 | NP_963845.1 | ||
NELL1 | NM_001288714.1 | c.245G>T | p.Arg82Leu | missense_variant | Exon 3 of 19 | NP_001275643.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461732Hom.: 0 Cov.: 41 AF XY: 0.00000275 AC XY: 2AN XY: 727172
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at