rs10139065
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000553776.1(BLZF2P):n.588C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.706 in 439,280 control chromosomes in the GnomAD database, including 110,805 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 0.69 ( 36051 hom., cov: 29)
Exomes 𝑓: 0.71 ( 74754 hom. )
Consequence
BLZF2P
ENST00000553776.1 non_coding_transcript_exon
ENST00000553776.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.45
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=-0.64).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.758 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 |
---|---|---|---|---|---|---|---|---|---|
BLZF2P | ENST00000553776.1 | n.588C>T | non_coding_transcript_exon_variant | 3/4 |
Frequencies
GnomAD3 genomes ? AF: 0.690 AC: 104004AN: 150626Hom.: 36020 Cov.: 29
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GnomAD4 exome AF: 0.714 AC: 206001AN: 288536Hom.: 74754 Cov.: 0 AF XY: 0.713 AC XY: 115165AN XY: 161492
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GnomAD4 genome ? AF: 0.690 AC: 104080AN: 150744Hom.: 36051 Cov.: 29 AF XY: 0.691 AC XY: 50808AN XY: 73482
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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