chr6-13294772-C-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001318809.2(TBC1D7-LOC100130357):c.*39+10290G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Consequence
TBC1D7-LOC100130357
NM_001318809.2 intron
NM_001318809.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.32
Publications
9 publications found
Genes affected
TBC1D7-LOC100130357 (HGNC:):
TBC1D7 (HGNC:21066): (TBC1 domain family member 7) This gene encodes a member of the TBC-domain containing protein family. The encoded protein functions as a subunit of the tuberous sclerosis TSC1-TSC2 complex which plays a role in the regulation of cellular growth and differentiation. Mutations in this gene have been associated with autosomal recessive megalencephaly. Alternative splicing results in multiple transcript variants. Naturally occurring readthrough transcription occurs between this locus and downstream LOC100130357. [provided by RefSeq, Jan 2016]
TBC1D7 Gene-Disease associations (from GenCC):
- macrocephaly/megalencephaly syndrome, autosomal recessiveInheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBC1D7-LOC100130357 | NM_001318809.2 | c.*39+10290G>T | intron_variant | Intron 8 of 8 | NP_001305738.1 | |||
TBC1D7-LOC100130357 | NR_134872.2 | n.712+24G>T | intron_variant | Intron 6 of 7 | ||||
LOC100130357 | NR_160971.1 | n.318+24G>T | intron_variant | Intron 3 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBC1D7 | ENST00000606214.5 | c.*39+10290G>T | intron_variant | Intron 7 of 7 | 5 | ENSP00000475727.1 | ||||
TBC1D7 | ENST00000421203.6 | n.*82+24G>T | intron_variant | Intron 6 of 7 | 2 | ENSP00000401438.2 | ||||
ENSG00000215022 | ENST00000606150.5 | n.318+24G>T | intron_variant | Intron 3 of 4 | 2 | |||||
ENSG00000215022 | ENST00000612479.1 | n.140+24G>T | intron_variant | Intron 2 of 3 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 17
GnomAD4 exome
Cov.:
17
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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