12-44522167-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001145108.2(NELL2):c.2008G>A(p.Val670Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000868 in 1,612,258 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NELL2 | NM_001145108.2 | c.2008G>A | p.Val670Ile | missense_variant | Exon 18 of 20 | ENST00000429094.7 | NP_001138580.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152002Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460256Hom.: 0 Cov.: 31 AF XY: 0.00000964 AC XY: 7AN XY: 726442
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74218
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2158G>A (p.V720I) 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 2158, causing the valine (V) at amino acid position 720 to be replaced by an isoleucine (I). 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