rs1377002
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001145108.2(NELL2):c.*144T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 694,962 control chromosomes in the GnomAD database, including 25,710 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.20 ( 4374 hom., cov: 32)
Exomes 𝑓: 0.25 ( 21336 hom. )
Consequence
NELL2
NM_001145108.2 3_prime_UTR
NM_001145108.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.499
Genes affected
NELL2 (HGNC:7751): (neural EGFL like 2) The protein encoded by this gene is a glycoprotein containing several von Willebrand factor C domains and epidermal growth factor (EGF)-like domains. The encoded protein acts as a homotrimer and is found in the cytoplasm. Several variants encoding a few different isoforms exist, and at least one isoform appears to be a secreted protein. Studies in mouse suggest that this protein plays a role in neural cell growth and differentiation as well as in oncogenesis. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NELL2 | NM_001145108.2 | c.*144T>C | 3_prime_UTR_variant | 20/20 | ENST00000429094.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NELL2 | ENST00000429094.7 | c.*144T>C | 3_prime_UTR_variant | 20/20 | 1 | NM_001145108.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.199 AC: 30247AN: 152012Hom.: 4364 Cov.: 32
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GnomAD4 exome AF: 0.254 AC: 138028AN: 542832Hom.: 21336 Cov.: 7 AF XY: 0.262 AC XY: 74212AN XY: 283530
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GnomAD4 genome ? AF: 0.199 AC: 30261AN: 152130Hom.: 4374 Cov.: 32 AF XY: 0.210 AC XY: 15624AN XY: 74364
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at