rs3840846
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The ENST00000351217.10(NPTN):c.-463del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0146 in 156,178 control chromosomes in the GnomAD database, including 28 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.015 ( 27 hom., cov: 32)
Exomes 𝑓: 0.014 ( 1 hom. )
Consequence
NPTN
ENST00000351217.10 5_prime_UTR
ENST00000351217.10 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.822
Genes affected
NPTN (HGNC:17867): (neuroplastin) This gene encodes a type I transmembrane protein belonging to the Ig superfamily. The protein is believed to be involved in cell-cell interactions or cell-substrate interactions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0146 (2229/152352) while in subpopulation EAS AF= 0.0542 (281/5184). AF 95% confidence interval is 0.049. There are 27 homozygotes in gnomad4. There are 1107 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 2229 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPTN | ENST00000351217.10 | c.-463del | 5_prime_UTR_variant | 1/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0146 AC: 2228AN: 152234Hom.: 27 Cov.: 32
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GnomAD4 exome AF: 0.0136 AC: 52AN: 3826Hom.: 1 Cov.: 0 AF XY: 0.0124 AC XY: 27AN XY: 2174
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GnomAD4 genome ? AF: 0.0146 AC: 2229AN: 152352Hom.: 27 Cov.: 32 AF XY: 0.0149 AC XY: 1107AN XY: 74506
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at