rs10491074
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000654191.1(ENSG00000228566):n.517-1324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0761 in 152,226 control chromosomes in the GnomAD database, including 940 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 0.076 ( 940 hom., cov: 32)
Consequence
ENSG00000228566
ENST00000654191.1 intron
ENST00000654191.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.675
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=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC124902439 | XR_007062160.1 | n.496-1324A>G | intron_variant | |||||
LOC124902439 | XR_007062161.1 | n.498-1324A>G | intron_variant | |||||
LOC124902439 | XR_007062163.1 | n.175-1324A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000228566 | ENST00000654191.1 | n.517-1324A>G | intron_variant | |||||||
ENSG00000228566 | ENST00000660795.1 | n.266-1324A>G | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.0759 AC: 11546AN: 152108Hom.: 936 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0761 AC: 11583AN: 152226Hom.: 940 Cov.: 32 AF XY: 0.0739 AC XY: 5502AN XY: 74428
GnomAD4 genome
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74428
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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