rs1856591
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_024472.1(RSU1P2):n.821-2671G>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 0.507 in 151,968 control chromosomes in the GnomAD database, including 19,778 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 0.51 ( 19778 hom., cov: 32)
Consequence
RSU1P2
NR_024472.1 intron, non_coding_transcript
NR_024472.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.102
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 (AMR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSU1P2 | NR_024472.1 | n.821-2671G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000448600.5 | n.570-2671G>A | intron_variant, non_coding_transcript_variant | 1 | ||||||
ENST00000619977.1 | n.821-2671G>A | intron_variant, non_coding_transcript_variant | 1 | ||||||
ENST00000661630.1 | n.508-2709G>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000423875.1 | n.1374-2671G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.507 AC: 76931AN: 151850Hom.: 19764 Cov.: 32
GnomAD3 genomes
?
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76931
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151850
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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: 0.507 AC: 76988AN: 151968Hom.: 19778 Cov.: 32 AF XY: 0.511 AC XY: 37926AN XY: 74288
GnomAD4 genome
?
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AC:
76988
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151968
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32
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37926
AN XY:
74288
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Asia WGS
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1547
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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