rs763110
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The variant allele was found at a frequency of 0.488 in 151,968 control chromosomes in the GnomAD database, including 21,522 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.49 ( 21522 hom., cov: 32)
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.80
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 1-172658358-C-T is Benign according to our data. Variant chr1-172658358-C-T is described in ClinVar as [Benign]. Clinvar id is 1165021.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
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Frequencies
GnomAD3 genomes AF: 0.488 AC: 74089AN: 151850Hom.: 21468 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: 0.488 AC: 74198AN: 151968Hom.: 21522 Cov.: 32 AF XY: 0.483 AC XY: 35845AN XY: 74270
GnomAD4 genome
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32
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35845
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74270
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Asia WGS
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1660
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Autoimmune lymphoproliferative syndrome type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 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