rs216345
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NR_170204.1(UBE2R2-AS1):n.373+411A>G 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 0.663 in 577,094 control chromosomes in the GnomAD database, including 121,044 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.66 ( 29270 hom., cov: 33)
Exomes 𝑓: 0.66 ( 91774 hom. )
Consequence
UBE2R2-AS1
NR_170204.1 intron, non_coding_transcript
NR_170204.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.85
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BP6
?
Variant 9-33799372-T-C is Benign according to our data. Variant chr9-33799372-T-C is described in ClinVar as [Benign]. Clinvar id is 1246185.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBE2R2-AS1 | NR_170204.1 | n.373+411A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBE2R2-AS1 | ENST00000705030.1 | n.235+415A>G | intron_variant, non_coding_transcript_variant | ||||||
UBE2R2-AS1 | ENST00000454429.2 | n.296+415A>G | intron_variant, non_coding_transcript_variant | 5 | |||||
UBE2R2-AS1 | ENST00000668091.1 | n.1295+415A>G | intron_variant, non_coding_transcript_variant | ||||||
UBE2R2-AS1 | ENST00000669609.1 | n.1400+415A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.656 AC: 94317AN: 143682Hom.: 29238 Cov.: 33
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GnomAD4 exome AF: 0.665 AC: 287962AN: 433292Hom.: 91774 AF XY: 0.665 AC XY: 148804AN XY: 223738
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GnomAD4 genome ? AF: 0.656 AC: 94403AN: 143802Hom.: 29270 Cov.: 33 AF XY: 0.660 AC XY: 46347AN XY: 70270
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 15, 2019 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at