17-79942077-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019020.4(TBC1D16):c.2038G>C(p.Glu680Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000974 in 1,611,982 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
TBC1D16
NM_019020.4 missense
NM_019020.4 missense
Scores
3
16
Clinical Significance
Conservation
PhyloP100: 5.51
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBC1D16 | NM_019020.4 | c.2038G>C | p.Glu680Gln | missense_variant | 11/12 | ENST00000310924.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D16 | ENST00000310924.7 | c.2038G>C | p.Glu680Gln | missense_variant | 11/12 | 1 | NM_019020.4 | P1 | |
TBC1D16 | ENST00000340848.11 | c.952G>C | p.Glu318Gln | missense_variant | 7/8 | 1 | |||
TBC1D16 | ENST00000576768.5 | c.913G>C | p.Glu305Gln | missense_variant | 7/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152160Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000323 AC: 8AN: 247704Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134580
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GnomAD4 exome AF: 0.000100 AC: 146AN: 1459822Hom.: 0 Cov.: 33 AF XY: 0.0000992 AC XY: 72AN XY: 726112
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GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74306
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2022 | The c.2038G>C (p.E680Q) alteration is located in exon 11 (coding exon 10) of the TBC1D16 gene. This alteration results from a G to C substitution at nucleotide position 2038, causing the glutamic acid (E) at amino acid position 680 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
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
Uncertain
D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N
REVEL
Benign
Sift
Benign
T;.;T
Sift4G
Benign
T;T;T
Polyphen
B;.;.
Vest4
MutPred
Gain of MoRF binding (P = 0.0234);.;.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Score
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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