rs10947885
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020737.3(LRFN2):c.1400+5055C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0256 in 152,274 control chromosomes in the GnomAD database, including 81 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 0.026 ( 81 hom., cov: 33)
Consequence
LRFN2
NM_020737.3 intron
NM_020737.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.91
Genes affected
LRFN2 (HGNC:21226): (leucine rich repeat and fibronectin type III domain containing 2) Predicted to be involved in modulation of chemical synaptic transmission and regulation of postsynapse organization. Predicted to be located in plasma membrane. Predicted to be active in Schaffer collateral - CA1 synapse and cell surface. Predicted to be integral component of postsynaptic density membrane. [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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0728 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRFN2 | NM_020737.3 | c.1400+5055C>T | intron_variant | ENST00000338305.7 | |||
LRFN2 | XM_011514762.3 | c.1400+5055C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRFN2 | ENST00000338305.7 | c.1400+5055C>T | intron_variant | 1 | NM_020737.3 | P1 | |||
LRFN2 | ENST00000700335.1 | c.1400+5055C>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0255 AC: 3881AN: 152156Hom.: 77 Cov.: 33
GnomAD3 genomes
?
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3881
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152156
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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: 0.0256 AC: 3894AN: 152274Hom.: 81 Cov.: 33 AF XY: 0.0270 AC XY: 2012AN XY: 74456
GnomAD4 genome
?
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3894
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152274
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33
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2012
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74456
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Asia WGS
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181
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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