rs1342022
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_929928.2(LOC105376081):n.1622C>T 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 0.573 in 151,862 control chromosomes in the GnomAD database, including 26,992 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 0.57 ( 26992 hom., cov: 32)
Consequence
LOC105376081
XR_929928.2 non_coding_transcript_exon
XR_929928.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.295
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=-1.0).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105376081 | XR_929928.2 | n.1622C>T | non_coding_transcript_exon_variant | 3/3 | |||
LOC105376081 | XR_929926.2 | n.1813C>T | non_coding_transcript_exon_variant | 4/4 | |||
LOC105376081 | XR_929927.2 | n.1750C>T | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes ? AF: 0.573 AC: 86906AN: 151744Hom.: 26980 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.573 AC: 86965AN: 151862Hom.: 26992 Cov.: 32 AF XY: 0.578 AC XY: 42903AN XY: 74208
GnomAD4 genome
?
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86965
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151862
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32
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42903
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74208
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1900
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3468
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