chr11-20847624-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006157.5(NELL1):c.377G>A(p.Arg126Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,580 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R126W) has been classified as Uncertain significance.
Frequency
Consequence
NM_006157.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NELL1 | NM_006157.5 | c.377G>A | p.Arg126Gln | missense_variant | 4/20 | ENST00000357134.10 | |
NELL1 | NM_001288713.1 | c.461G>A | p.Arg154Gln | missense_variant | 5/21 | ||
NELL1 | NM_201551.2 | c.377G>A | p.Arg126Gln | missense_variant | 4/19 | ||
NELL1 | NM_001288714.1 | c.336-37820G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NELL1 | ENST00000357134.10 | c.377G>A | p.Arg126Gln | missense_variant | 4/20 | 1 | NM_006157.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152098Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000718 AC: 18AN: 250844Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135556
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461482Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727048
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152098Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2023 | The c.377G>A (p.R126Q) alteration is located in exon 4 (coding exon 4) of the NELL1 gene. This alteration results from a G to A substitution at nucleotide position 377, causing the arginine (R) at amino acid position 126 to be replaced by a glutamine (Q). 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