17-36260264-C-G

Position:

• chr17-36260264-C-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Moderate BP6_Moderate

The NM_001291463.2(TBC1D3I):​c.352G>C​(p.Glu118Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 4/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TBC1D3I NM_001291463.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.247

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.08245078).
• BP6: Variant 17-36260264-C-G is Benign according to our data. Variant chr17-36260264-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3026038.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBC1D3I	NM_001291463.2	c.352G>C	p.Glu118Gln	missense_variant	6/14	ENST00000621034.2	NP_001278392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBC1D3I	ENST00000621034.2	c.352G>C	p.Glu118Gln	missense_variant	6/14	1	NM_001291463.2	ENSP00000481258	P1
TBC1D3I	ENST00000618620.4	c.352G>C	p.Glu118Gln	missense_variant	6/12	1		ENSP00000479474
TBC1D3I	ENST00000616671.4	c.352G>C	p.Glu118Gln	missense_variant	5/11	5		ENSP00000482914

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 339574 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 169610

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2024

TBC1D3C: BS2; TBC1D3I: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
CADD	Benign	0.073
DEOGEN2	Benign	0.0022	.;.;T
MetaRNN	Benign	0.082	T;T;T
Sift4G	Benign	0.58	T;T;T
Vest4		0.11
gMVP		0.019

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1597756146; hg19: -;