11-20678032-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006157.5(NELL1):c.156C>G(p.His52Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. H52Y) 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NELL1 | NM_006157.5 | c.156C>G | p.His52Gln | missense_variant | Exon 2 of 20 | ENST00000357134.10 | NP_006148.2 | |
NELL1 | NM_001288713.1 | c.240C>G | p.His80Gln | missense_variant | Exon 3 of 21 | NP_001275642.1 | ||
NELL1 | NM_201551.2 | c.156C>G | p.His52Gln | missense_variant | Exon 2 of 19 | NP_963845.1 | ||
NELL1 | NM_001288714.1 | c.156C>G | p.His52Gln | missense_variant | Exon 2 of 19 | NP_001275643.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NELL1 | ENST00000357134.10 | c.156C>G | p.His52Gln | missense_variant | Exon 2 of 20 | 1 | NM_006157.5 | ENSP00000349654.5 | ||
NELL1 | ENST00000532434.5 | c.156C>G | p.His52Gln | missense_variant | Exon 2 of 19 | 1 | ENSP00000437170.1 | |||
NELL1 | ENST00000298925.9 | c.240C>G | p.His80Gln | missense_variant | Exon 3 of 21 | 2 | ENSP00000298925.5 | |||
NELL1 | ENST00000325319.9 | c.156C>G | p.His52Gln | missense_variant | Exon 2 of 19 | 2 | ENSP00000317837.5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.156C>G (p.H52Q) alteration is located in exon 2 (coding exon 2) of the NELL1 gene. This alteration results from a C to G substitution at nucleotide position 156, causing the histidine (H) at amino acid position 52 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