rs10423751
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The 19-54713465-T-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00054 in 198,144 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00059 ( 0 hom., cov: 28)
Exomes 𝑓: 0.00039 ( 0 hom. )
Consequence
LILRP2
NR_003061.2 downstream_gene
NR_003061.2 downstream_gene
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.41
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (Cadd=0.311).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LILRP2 | NR_003061.2 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LILRP2 | ENST00000413439.5 | downstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000587 AC: 89AN: 151586Hom.: 0 Cov.: 28
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GnomAD4 exome AF: 0.000388 AC: 18AN: 46440Hom.: 0 Cov.: 0 AF XY: 0.000450 AC XY: 11AN XY: 24448
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GnomAD4 genome ? AF: 0.000587 AC: 89AN: 151704Hom.: 0 Cov.: 28 AF XY: 0.000513 AC XY: 38AN XY: 74122
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ClinVar
Not reported inComputational scores
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Name
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Prediction
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at