2-101018907-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001330348.2(TBC1D8):c.2827+2774C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,517,224 control chromosomes in the GnomAD database, including 12,921 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.10 ( 948 hom., cov: 33)
Exomes 𝑓: 0.13 ( 11973 hom. )
Consequence
TBC1D8
NM_001330348.2 intron
NM_001330348.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0440
Genes affected
TBC1D8 (HGNC:17791): (TBC1 domain family member 8) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
RPL31 (HGNC:10334): (ribosomal protein L31) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L31E family of ribosomal proteins. It is located in the cytoplasm. Higher levels of expression of this gene in familial adenomatous polyps compared to matched normal tissues have been observed. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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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 (BayesDel_noAF=-0.91).
BP6
?
Variant 2-101018907-G-A is Benign according to our data. Variant chr2-101018907-G-A is described in ClinVar as [Benign]. Clinvar id is 1183797.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBC1D8 | NM_001330348.2 | c.2827+2774C>T | intron_variant | ENST00000409318.2 | |||
RPL31 | NM_001098577.3 | c.347-91G>A | intron_variant | ||||
TBC1D8 | NM_001102426.3 | c.2782+2774C>T | intron_variant | ||||
TBC1D8 | NR_138475.2 | n.2793+2774C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D8 | ENST00000409318.2 | c.2827+2774C>T | intron_variant | 5 | NM_001330348.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.104 AC: 15821AN: 152136Hom.: 947 Cov.: 33
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GnomAD4 exome AF: 0.126 AC: 171428AN: 1364970Hom.: 11973 AF XY: 0.123 AC XY: 83138AN XY: 673700
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GnomAD4 genome ? AF: 0.104 AC: 15835AN: 152254Hom.: 948 Cov.: 33 AF XY: 0.104 AC XY: 7748AN XY: 74454
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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 | GeneDx | May 17, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at