chr11-66838438-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001302084.2(C11orf80):c.1242C>T(p.Leu414=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0017 in 1,613,690 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0089 ( 23 hom., cov: 32)
Exomes 𝑓: 0.00095 ( 20 hom. )
Consequence
C11orf80
NM_001302084.2 synonymous
NM_001302084.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0190
Genes affected
C11orf80 (HGNC:26197): (TOP6B like initiator of meiotic double strand breaks) Predicted to be involved in meiotic DNA double-strand break formation and reciprocal meiotic recombination. Predicted to be located in chromosome. Implicated in gestational trophoblastic neoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 11-66838438-C-T is Benign according to our data. Variant chr11-66838438-C-T is described in ClinVar as [Benign]. Clinvar id is 3049948.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.019 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00887 (1351/152272) while in subpopulation AFR AF= 0.0302 (1257/41554). AF 95% confidence interval is 0.0289. There are 23 homozygotes in gnomad4. There are 614 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 23 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C11orf80 | NM_001302084.2 | c.1242C>T | p.Leu414= | synonymous_variant | 13/15 | ENST00000540737.7 | |
C11orf80 | NM_024650.3 | c.1740C>T | p.Leu580= | synonymous_variant | 15/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C11orf80 | ENST00000540737.7 | c.1242C>T | p.Leu414= | synonymous_variant | 13/15 | 2 | NM_001302084.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00886 AC: 1348AN: 152154Hom.: 23 Cov.: 32
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GnomAD3 exomes AF: 0.00238 AC: 594AN: 249088Hom.: 9 AF XY: 0.00164 AC XY: 221AN XY: 135140
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GnomAD4 exome AF: 0.000950 AC: 1388AN: 1461418Hom.: 20 Cov.: 30 AF XY: 0.000795 AC XY: 578AN XY: 727002
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GnomAD4 genome ? AF: 0.00887 AC: 1351AN: 152272Hom.: 23 Cov.: 32 AF XY: 0.00824 AC XY: 614AN XY: 74472
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TOP6BL-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at