rs1267053
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The variant allele was found at a frequency of 0.0257 in 152,150 control chromosomes in the GnomAD database, including 177 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 0.026 ( 177 hom., cov: 31)
Exomes 𝑓: 0.018 ( 0 hom. )
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.752
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0859 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
use as main transcript | n.161254721C>G | intergenic_region |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSMD14-DT | ENST00000435692.6 | n.344-41G>C | intron_variant | 5 | ||||||
PSMD14-DT | ENST00000628042.2 | n.344-3499G>C | intron_variant | 5 | ||||||
PSMD14-DT | ENST00000628613.2 | n.574-3517G>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0257 AC: 3904AN: 151976Hom.: 178 Cov.: 31
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GnomAD4 exome AF: 0.0179 AC: 1AN: 56Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 42
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GnomAD4 genome AF: 0.0257 AC: 3912AN: 152094Hom.: 177 Cov.: 31 AF XY: 0.0253 AC XY: 1882AN XY: 74342
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at