rs12655019
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_948347.4(LOC105378980):n.70+34T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0921 in 152,266 control chromosomes in the GnomAD database, including 652 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 0.092 ( 652 hom., cov: 32)
Exomes 𝑓: 0.065 ( 0 hom. )
Consequence
LOC105378980
XR_948347.4 intron, non_coding_transcript
XR_948347.4 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0820
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=-0.96).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105378980 | XR_948347.4 | n.70+34T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.0922 AC: 14018AN: 152102Hom.: 651 Cov.: 32
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GnomAD4 exome AF: 0.0652 AC: 3AN: 46Hom.: 0 AF XY: 0.0882 AC XY: 3AN XY: 34
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GnomAD4 genome ? AF: 0.0921 AC: 14027AN: 152220Hom.: 652 Cov.: 32 AF XY: 0.0925 AC XY: 6883AN XY: 74446
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at