rs11852150
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The 14-21163764-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 780,232 control chromosomes in the GnomAD database, including 23,087 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 0.29 ( 7703 hom., cov: 31)
Exomes 𝑓: 0.21 ( 15384 hom. )
Consequence
SMARCE1P3
ENST00000553649.2 downstream_gene
ENST00000553649.2 downstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.884
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=-0.71).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCE1P3 | ENST00000553649.2 | downstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.289 AC: 43800AN: 151718Hom.: 7679 Cov.: 31
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GnomAD4 exome AF: 0.213 AC: 133995AN: 628396Hom.: 15384 Cov.: 8 AF XY: 0.211 AC XY: 71779AN XY: 339570
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GnomAD4 genome ? AF: 0.289 AC: 43880AN: 151836Hom.: 7703 Cov.: 31 AF XY: 0.285 AC XY: 21180AN XY: 74194
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at