rs11721044
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001365925.2(NLGN1):c.-321+39270T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,130 control chromosomes in the GnomAD database, including 3,458 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 0.17 ( 3458 hom., cov: 32)
Consequence
NLGN1
NM_001365925.2 intron
NM_001365925.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.907
Genes affected
NLGN1 (HGNC:14291): (neuroligin 1) This gene encodes a member of a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. [provided by RefSeq, Jul 2008]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLGN1 | NM_001365925.2 | c.-321+39270T>C | intron_variant | ENST00000695368.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLGN1 | ENST00000695368.1 | c.-321+39270T>C | intron_variant | NM_001365925.2 | A1 | ||||
NLGN1 | ENST00000457714.5 | c.-321+2255T>C | intron_variant | 1 | P2 | ||||
NLGN1 | ENST00000413821.1 | c.-321+39270T>C | intron_variant | 4 | |||||
NLGN1 | ENST00000423427.1 | c.-321+40638T>C | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.173 AC: 26289AN: 152010Hom.: 3447 Cov.: 32
GnomAD3 genomes
?
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152010
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.173 AC: 26322AN: 152130Hom.: 3458 Cov.: 32 AF XY: 0.168 AC XY: 12529AN XY: 74384
GnomAD4 genome
?
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26322
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152130
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32
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12529
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74384
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221
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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