12-44522007-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001145108.2(NELL2):c.2168G>A(p.Arg723His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,612,736 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145108.2 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 |
---|---|---|---|---|---|---|---|---|
NELL2 | NM_001145108.2 | c.2168G>A | p.Arg723His | missense_variant | Exon 18 of 20 | ENST00000429094.7 | NP_001138580.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151956Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249884Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134964
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1460780Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726628
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151956Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74216
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2318G>A (p.R773H) alteration is located in exon 19 (coding exon 19) of the NELL2 gene. This alteration results from a G to A substitution at nucleotide position 2318, causing the arginine (R) at amino acid position 773 to be replaced by a histidine (H). 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