rs10512160
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The variant allele was found at a frequency of 0.0312 in 152,276 control chromosomes in the GnomAD database, including 68 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 0.031 ( 68 hom., cov: 33)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.428
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0312 (4748/152276) while in subpopulation SAS AF= 0.0458 (221/4822). AF 95% confidence interval is 0.0409. There are 68 homozygotes in gnomad4. There are 2388 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 68 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.0312 AC: 4742AN: 152158Hom.: 68 Cov.: 33
GnomAD3 genomes
?
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AC:
4742
AN:
152158
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Cov.:
33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0312 AC: 4748AN: 152276Hom.: 68 Cov.: 33 AF XY: 0.0321 AC XY: 2388AN XY: 74466
GnomAD4 genome
?
AF:
AC:
4748
AN:
152276
Hom.:
Cov.:
33
AF XY:
AC XY:
2388
AN XY:
74466
Gnomad4 AFR
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Asia WGS
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AC:
99
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