rs3810171
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The 19-41193088-C-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0802 in 1,015,514 control chromosomes in the GnomAD database, including 3,836 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 0.10 ( 859 hom., cov: 32)
Exomes 𝑓: 0.077 ( 2977 hom. )
Consequence
LOC124904790
XM_047439802.1 upstream_gene
XM_047439802.1 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.143
Genes affected
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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=-0.76).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124904790 | XM_047439802.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.100 AC: 15230AN: 152040Hom.: 856 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome AF: 0.0767 AC: 66198AN: 863356Hom.: 2977 Cov.: 12 AF XY: 0.0782 AC XY: 33284AN XY: 425432
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GnomAD4 genome ? AF: 0.100 AC: 15253AN: 152158Hom.: 859 Cov.: 32 AF XY: 0.102 AC XY: 7558AN XY: 74380
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513
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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