rs940850
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_004822.3(NTN1):c.1018+3372C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 151,678 control chromosomes in the GnomAD database, including 1,187 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 0.11 ( 1187 hom., cov: 31)
Consequence
NTN1
NM_004822.3 intron
NM_004822.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.58
Genes affected
NTN1 (HGNC:8029): (netrin 1) Netrin is included in a family of laminin-related secreted proteins. The function of this gene has not yet been defined; however, netrin is thought to be involved in axon guidance and cell migration during development. Mutations and loss of expression of netrin suggest that variation in netrin may be involved in cancer development. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NTN1 | NM_004822.3 | c.1018+3372C>T | intron_variant | ENST00000173229.7 | |||
NTN1 | XM_006721595.4 | c.1018+3372C>T | intron_variant | ||||
NTN1 | XM_047437096.1 | c.1018+3372C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NTN1 | ENST00000173229.7 | c.1018+3372C>T | intron_variant | 1 | NM_004822.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.114 AC: 17243AN: 151560Hom.: 1174 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.114 AC: 17292AN: 151678Hom.: 1187 Cov.: 31 AF XY: 0.115 AC XY: 8541AN XY: 74070
GnomAD4 genome
?
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31
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8541
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74070
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696
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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