rs9838229
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000485055.5(ENSG00000285336):n.251-4993G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,190 control chromosomes in the GnomAD database, including 49,064 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 0.80 ( 49064 hom., cov: 33)
Consequence
ENSG00000285336
ENST00000485055.5 intron
ENST00000485055.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.584
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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC101928882 | NR_109986.1 | n.251-4993G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000285336 | ENST00000485055.5 | n.251-4993G>T | intron_variant | 1 | ||||||
ENSG00000145075 | ENST00000471307.6 | n.252+32044G>T | intron_variant | 3 | ||||||
ENSG00000285336 | ENST00000495817.1 | n.207-33339G>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.798 AC: 121338AN: 152072Hom.: 49020 Cov.: 33
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GnomAD4 genome AF: 0.798 AC: 121436AN: 152190Hom.: 49064 Cov.: 33 AF XY: 0.799 AC XY: 59480AN XY: 74414
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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