rs200360214
Positions:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_020461.4(TUBGCP6):āc.245T>Gā(p.Leu82Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000279 in 1,613,346 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.000079 ( 0 hom., cov: 32)
Exomes š: 0.000023 ( 0 hom. )
Consequence
TUBGCP6
NM_020461.4 missense
NM_020461.4 missense
Scores
7
12
Clinical Significance
Conservation
PhyloP100: 3.79
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.020662546).
BP6
?
Variant 22-50244215-A-C is Benign according to our data. Variant chr22-50244215-A-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 437162.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000788 (12/152366) while in subpopulation EAS AF= 0.00231 (12/5190). AF 95% confidence interval is 0.00133. There are 0 homozygotes in gnomad4. There are 10 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.245T>G | p.Leu82Arg | missense_variant | 1/25 | ENST00000248846.10 | |
TUBGCP6 | XR_001755343.3 | n.809T>G | non_coding_transcript_exon_variant | 1/20 | |||
TUBGCP6 | XR_007067982.1 | n.809T>G | non_coding_transcript_exon_variant | 1/19 | |||
TUBGCP6 | XR_938347.3 | n.809T>G | non_coding_transcript_exon_variant | 1/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.245T>G | p.Leu82Arg | missense_variant | 1/25 | 1 | NM_020461.4 | P1 | |
TUBGCP6 | ENST00000439308.6 | c.245T>G | p.Leu82Arg | missense_variant | 1/25 | 1 | |||
TUBGCP6 | ENST00000498611.5 | n.778T>G | non_coding_transcript_exon_variant | 1/23 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152248Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000152 AC: 38AN: 250794Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135736
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GnomAD4 exome AF: 0.0000226 AC: 33AN: 1460980Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 726770
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GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74516
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 31, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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