rs3759171
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001146213.3(TBC1D15):āc.1311A>Gā(p.Gln437=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 1,564,336 control chromosomes in the GnomAD database, including 122,381 homozygotes. 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: š 0.50 ( 24503 hom., cov: 32)
Exomes š: 0.34 ( 97878 hom. )
Consequence
TBC1D15
NM_001146213.3 synonymous
NM_001146213.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.71
Genes affected
TBC1D15 (HGNC:25694): (TBC1 domain family member 15) This gene encodes a member of the Ras-like proteins in brain-GTPase activating protein superfamily that share a conserved Tre-2/Bub2/Cdc16 domain. The encoded protein interacts with Ras-like protein in brain 5A and may function as a regulator of intracellular trafficking. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP7
Synonymous conserved (PhyloP=2.71 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBC1D15 | NM_001146213.3 | c.1311A>G | p.Gln437= | synonymous_variant | 12/17 | ENST00000485960.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D15 | ENST00000485960.7 | c.1311A>G | p.Gln437= | synonymous_variant | 12/17 | 1 | NM_001146213.3 | P3 |
Frequencies
GnomAD3 genomes AF: 0.502 AC: 76201AN: 151724Hom.: 24428 Cov.: 32
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GnomAD3 exomes AF: 0.436 AC: 91331AN: 209374Hom.: 25311 AF XY: 0.418 AC XY: 47848AN XY: 114486
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GnomAD4 exome AF: 0.338 AC: 477919AN: 1412494Hom.: 97878 Cov.: 29 AF XY: 0.341 AC XY: 239793AN XY: 702844
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GnomAD4 genome AF: 0.503 AC: 76335AN: 151842Hom.: 24503 Cov.: 32 AF XY: 0.509 AC XY: 37780AN XY: 74216
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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