rs79913282
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NR_109951.1(OSMR-DT):n.162+862G>A 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 0.00424 in 151,588 control chromosomes in the GnomAD database, including 12 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 0.0042 ( 12 hom., cov: 32)
Consequence
OSMR-DT
NR_109951.1 intron, non_coding_transcript
NR_109951.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.19
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BS2
?
High Homozygotes in GnomAd4 at 12 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OSMR-DT | NR_109951.1 | n.162+862G>A | intron_variant, non_coding_transcript_variant | ||||
OSMR-DT | NR_171676.1 | n.102+862G>A | intron_variant, non_coding_transcript_variant | ||||
OSMR-DT | NR_171677.1 | n.102+862G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OSMR-DT | ENST00000662290.1 | n.126+862G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00423 AC: 640AN: 151464Hom.: 12 Cov.: 32
GnomAD3 genomes
?
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640
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00424 AC: 642AN: 151588Hom.: 12 Cov.: 32 AF XY: 0.00401 AC XY: 297AN XY: 74046
GnomAD4 genome
?
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642
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32
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297
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74046
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3478
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