17-36257860-C-T

Variant names:

• chr17-36257860-C-T
• rs1271180360
• NM_001291463.2:c.636G>A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.10

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 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
TBC1D3I	NM_001291463.2	c.636G>A	p.Gln212Gln	synonymous_variant	Exon 9 of 14	ENST00000621034.2	NP_001278392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBC1D3I	ENST00000621034.2	c.636G>A	p.Gln212Gln	synonymous_variant	Exon 9 of 14	1	NM_001291463.2	ENSP00000481258.1
TBC1D3I	ENST00000618620.4	c.636G>A	p.Gln212Gln	synonymous_variant	Exon 9 of 12	1		ENSP00000479474.1
TBC1D3I	ENST00000616671.4	c.636G>A	p.Gln212Gln	synonymous_variant	Exon 8 of 11	5		ENSP00000482914.1

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

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

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

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

Other links and lift over

dbSNP: rs1271180360; hg19: chr17-34585324;