17-36257860-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001291463.2(TBC1D3I):​c.636G>A​(p.Gln212Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 3)
Exomes 𝑓: 0.0000095 ( 1 hom. )
Failed GnomAD Quality Control

Consequence

TBC1D3I
NM_001291463.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.10
Variant links:
Genes affected
TBC1D3I (HGNC:32709): (TBC1 domain family member 3I) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 17-36257860-C-T is Benign according to our data. Variant chr17-36257860-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3388612.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.1 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TBC1D3INM_001291463.2 linkc.636G>A p.Gln212Gln synonymous_variant Exon 9 of 14 ENST00000621034.2 NP_001278392.1 A0A087WXS9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TBC1D3IENST00000621034.2 linkc.636G>A p.Gln212Gln synonymous_variant Exon 9 of 14 1 NM_001291463.2 ENSP00000481258.1 A0A087WXS9
TBC1D3IENST00000618620.4 linkc.636G>A p.Gln212Gln synonymous_variant Exon 9 of 12 1 ENSP00000479474.1 A0A0B4J2F4
TBC1D3IENST00000616671.4 linkc.636G>A p.Gln212Gln synonymous_variant Exon 8 of 11 5 ENSP00000482914.1 A0A0B4J2F4

Frequencies

GnomAD3 genomes
Cov.:
3
GnomAD3 exomes
AF:
0.000223
AC:
3
AN:
13456
Hom.:
0
AF XY:
0.000149
AC XY:
1
AN XY:
6700
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000175
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00641
Gnomad NFE exome
AF:
0.000452
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000947
AC:
2
AN:
211106
Hom.:
1
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
113052
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000191
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
3

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Nov 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

TBC1D3I: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.60
CADD
Benign
2.1
DANN
Benign
0.92

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1271180360; hg19: chr17-34585324; API