11-126160720-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The ENST00000532357.1(ENSG00000254833):n.7G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 152,318 control chromosomes in the GnomAD database, including 674 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 0.078 ( 673 hom., cov: 33)
Exomes 𝑓: 0.033 ( 1 hom. )
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.06
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 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 |
---|---|---|---|---|---|---|---|---|---|
ENST00000532357.1 | n.7G>A | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0778 AC: 11840AN: 152140Hom.: 671 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.0333 AC: 2AN: 60Hom.: 1 Cov.: 0 AF XY: 0.0556 AC XY: 2AN XY: 36
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GnomAD4 genome ? AF: 0.0779 AC: 11854AN: 152258Hom.: 673 Cov.: 33 AF XY: 0.0816 AC XY: 6076AN XY: 74450
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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