rs12305135
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000505807.6(FZD10-AS1):n.3848A>G 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 0.071 in 152,324 control chromosomes in the GnomAD database, including 498 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 0.071 ( 498 hom., cov: 34)
Exomes 𝑓: 0.091 ( 0 hom. )
Consequence
FZD10-AS1
ENST00000505807.6 non_coding_transcript_exon
ENST00000505807.6 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.433
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 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 |
---|---|---|---|---|---|---|---|---|---|
FZD10-AS1 | ENST00000505807.6 | n.3848A>G | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0709 AC: 10790AN: 152184Hom.: 500 Cov.: 34
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GnomAD4 exome AF: 0.0909 AC: 2AN: 22Hom.: 0 Cov.: 0 AF XY: 0.111 AC XY: 2AN XY: 18
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GnomAD4 genome ? AF: 0.0710 AC: 10807AN: 152302Hom.: 498 Cov.: 34 AF XY: 0.0753 AC XY: 5609AN XY: 74470
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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