chr15-89582933-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_152259.4(TICRR):c.902G>A(p.Arg301Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00172 in 1,613,536 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 9 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 73 hom. )
Consequence
TICRR
NM_152259.4 missense
NM_152259.4 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 0.0570
Genes affected
TICRR (HGNC:28704): (TOPBP1 interacting checkpoint and replication regulator) Enables chromatin binding activity. Involved in regulation of DNA-dependent DNA replication initiation. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0028099418).
BP6
?
Variant 15-89582933-G-A is Benign according to our data. Variant chr15-89582933-G-A is described in ClinVar as [Benign]. Clinvar id is 782310.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00245 (372/151972) while in subpopulation AMR AF= 0.0212 (323/15264). AF 95% confidence interval is 0.0193. There are 9 homozygotes in gnomad4. There are 189 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TICRR | NM_152259.4 | c.902G>A | p.Arg301Gln | missense_variant | 2/22 | ENST00000268138.12 | |
TICRR | NM_001308025.1 | c.902G>A | p.Arg301Gln | missense_variant | 2/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TICRR | ENST00000268138.12 | c.902G>A | p.Arg301Gln | missense_variant | 2/22 | 5 | NM_152259.4 | A2 | |
TICRR | ENST00000560985.5 | c.902G>A | p.Arg301Gln | missense_variant | 2/22 | 1 | P4 | ||
ENST00000559041.1 | n.48-8570G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00245 AC: 372AN: 151866Hom.: 9 Cov.: 33
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GnomAD3 exomes AF: 0.00748 AC: 1864AN: 249300Hom.: 55 AF XY: 0.00547 AC XY: 740AN XY: 135290
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GnomAD4 exome AF: 0.00165 AC: 2406AN: 1461564Hom.: 73 Cov.: 37 AF XY: 0.00136 AC XY: 988AN XY: 727036
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GnomAD4 genome ? AF: 0.00245 AC: 372AN: 151972Hom.: 9 Cov.: 33 AF XY: 0.00255 AC XY: 189AN XY: 74262
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at