rs12551232
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The variant allele was found at a frequency of 0.135 in 613,924 control chromosomes in the GnomAD database, including 6,974 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.17 ( 2806 hom., cov: 34)
Exomes 𝑓: 0.12 ( 4168 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.17
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 9-35658073-T-C is Benign according to our data. Variant chr9-35658073-T-C is described in ClinVar as [Benign]. Clinvar id is 138921.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.
Transcripts
RefSeq
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Ensembl
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Frequencies
GnomAD3 genomes ? AF: 0.171 AC: 26035AN: 152034Hom.: 2789 Cov.: 34
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GnomAD4 exome AF: 0.123 AC: 57008AN: 461772Hom.: 4168 Cov.: 0 AF XY: 0.121 AC XY: 29672AN XY: 244216
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GnomAD4 genome ? AF: 0.172 AC: 26099AN: 152152Hom.: 2806 Cov.: 34 AF XY: 0.165 AC XY: 12288AN XY: 74398
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Metaphyseal chondrodysplasia, McKusick type Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Anauxetic dysplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational 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