rs13387838
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 0.0139 in 152,272 control chromosomes in the GnomAD database, including 28 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 0.014 ( 28 hom., cov: 31)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0180
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0139 (2123/152272) while in subpopulation AMR AF= 0.0205 (314/15302). AF 95% confidence interval is 0.0187. There are 28 homozygotes in gnomad4. There are 994 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 28 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: 0.0140 AC: 2124AN: 152154Hom.: 28 Cov.: 31
GnomAD3 genomes
?
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2124
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152154
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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: 0.0139 AC: 2123AN: 152272Hom.: 28 Cov.: 31 AF XY: 0.0134 AC XY: 994AN XY: 74448
GnomAD4 genome
?
AF:
AC:
2123
AN:
152272
Hom.:
Cov.:
31
AF XY:
AC XY:
994
AN XY:
74448
Gnomad4 AFR
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Asia WGS
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1
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