rs10946675
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_080723.5(NRSN1):c.190-3856G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,098 control chromosomes in the GnomAD database, including 15,778 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 0.42 ( 15778 hom., cov: 33)
Consequence
NRSN1
NM_080723.5 intron
NM_080723.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.755
Genes affected
NRSN1 (HGNC:17881): (neurensin 1) Predicted to be involved in nervous system development. Predicted to be located in cytoplasmic vesicle and growth cone. Predicted to be active in neuron projection; neuronal cell body; and transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.8).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRSN1 | NM_080723.5 | c.190-3856G>A | intron_variant | ENST00000378491.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRSN1 | ENST00000378491.9 | c.190-3856G>A | intron_variant | 1 | NM_080723.5 | P1 | |||
NRSN1 | ENST00000378477.2 | c.190-3856G>A | intron_variant | 1 | |||||
NRSN1 | ENST00000378478.5 | c.190-3856G>A | intron_variant | 1 | P1 | ||||
NRSN1 | ENST00000468195.2 | n.256+7176G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.425 AC: 64611AN: 151978Hom.: 15773 Cov.: 33
GnomAD3 genomes
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64611
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151978
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.425 AC: 64615AN: 152098Hom.: 15778 Cov.: 33 AF XY: 0.431 AC XY: 32024AN XY: 74340
GnomAD4 genome
?
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64615
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33
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32024
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1081
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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