rs10170138
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134745.3(LRRTM4):c.1552-45886G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,772 control chromosomes in the GnomAD database, including 2,037 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 0.16 ( 2037 hom., cov: 32)
Consequence
LRRTM4
NM_001134745.3 intron
NM_001134745.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.540
Genes affected
LRRTM4 (HGNC:19411): (leucine rich repeat transmembrane neuronal 4) Predicted to enable heparan sulfate proteoglycan binding activity. Predicted to be involved in regulation of synapse assembly. Predicted to act upstream of or within AMPA glutamate receptor clustering; positive regulation of synapse assembly; and regulation of presynaptic membrane organization. Predicted to be located in postsynaptic membrane. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in extracellular matrix; extracellular space; and glutamatergic synapse. 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=-0.95).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRTM4 | NM_001134745.3 | c.1552-45886G>A | intron_variant | ENST00000409884.6 | |||
LRRTM4 | NM_001282924.3 | c.1552-45886G>A | intron_variant | ||||
LRRTM4 | NM_001330370.2 | c.1555-45886G>A | intron_variant | ||||
LRRTM4 | NR_146416.2 | n.269-45886G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRTM4 | ENST00000409884.6 | c.1552-45886G>A | intron_variant | 1 | NM_001134745.3 | P4 | |||
LRRTM4 | ENST00000409093.1 | c.1552-45886G>A | intron_variant | 2 | P4 | ||||
LRRTM4 | ENST00000409911.5 | c.1555-45886G>A | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.157 AC: 23858AN: 151652Hom.: 2031 Cov.: 32
GnomAD3 genomes
?
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23858
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151652
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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: 0.157 AC: 23883AN: 151772Hom.: 2037 Cov.: 32 AF XY: 0.157 AC XY: 11658AN XY: 74162
GnomAD4 genome
?
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23883
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151772
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32
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11658
AN XY:
74162
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318
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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