rs2065914
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The 1-240007496-T-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,778 control chromosomes in the GnomAD database, including 11,754 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 0.39 ( 11754 hom., cov: 31)
Consequence
RPS7P5
NR_036695.2 upstream_gene
NR_036695.2 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.288
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS7P5 | NR_036695.2 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000668221.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.387 AC: 58736AN: 151660Hom.: 11755 Cov.: 31
GnomAD3 genomes
?
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58736
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151660
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.387 AC: 58746AN: 151778Hom.: 11754 Cov.: 31 AF XY: 0.385 AC XY: 28577AN XY: 74152
GnomAD4 genome
?
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AC:
58746
AN:
151778
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Cov.:
31
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28577
AN XY:
74152
Gnomad4 AFR
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Asia WGS
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967
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at