rs28373064
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_007066828.1(LOC124904492):n.99T>C 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 0.186 in 152,110 control chromosomes in the GnomAD database, including 2,882 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 0.19 ( 2881 hom., cov: 31)
Exomes 𝑓: 0.12 ( 1 hom. )
Consequence
LOC124904492
XR_007066828.1 non_coding_transcript_exon
XR_007066828.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.362
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=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124904492 | XR_007066828.1 | n.99T>C | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AVPR1B-DT | ENST00000425896.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.186 AC: 28285AN: 151924Hom.: 2877 Cov.: 31
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GnomAD4 exome AF: 0.121 AC: 8AN: 66Hom.: 1 Cov.: 0 AF XY: 0.104 AC XY: 5AN XY: 48
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GnomAD4 genome ? AF: 0.186 AC: 28316AN: 152044Hom.: 2881 Cov.: 31 AF XY: 0.187 AC XY: 13866AN XY: 74310
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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