rs17167492
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_144648.3(LRGUK):c.588+106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 706,352 control chromosomes in the GnomAD database, including 7,038 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 0.12 ( 1423 hom., cov: 33)
Exomes 𝑓: 0.13 ( 5615 hom. )
Consequence
LRGUK
NM_144648.3 intron
NM_144648.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.43
Genes affected
LRGUK (HGNC:21964): (leucine rich repeats and guanylate kinase domain containing) Predicted to enable guanylate kinase activity. Predicted to be involved in axoneme assembly and spermatogenesis. Predicted to be located in acrosomal vesicle and manchette. Predicted to be active in cytosol. [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=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRGUK | NM_144648.3 | c.588+106G>A | intron_variant | ENST00000285928.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRGUK | ENST00000285928.3 | c.588+106G>A | intron_variant | 1 | NM_144648.3 | P2 | |||
LRGUK | ENST00000645682.1 | c.588+106G>A | intron_variant | A2 | |||||
LRGUK | ENST00000695542.2 | c.588+106G>A | intron_variant | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.122 AC: 18476AN: 152030Hom.: 1420 Cov.: 33
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GnomAD4 exome AF: 0.126 AC: 69654AN: 554204Hom.: 5615 AF XY: 0.127 AC XY: 38028AN XY: 300108
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GnomAD4 genome ? AF: 0.122 AC: 18502AN: 152148Hom.: 1423 Cov.: 33 AF XY: 0.123 AC XY: 9121AN XY: 74382
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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