chr17-36257860-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 VariationId is 3388612.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=1.1 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001291463.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBC1D3I	NM_001291463.2	MANE Select	c.636G>A	p.Gln212Gln	synonymous	Exon 9 of 14	NP_001278392.1	A0A087WXS9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBC1D3I	ENST00000621034.2	TSL:1 MANE Select	c.636G>A	p.Gln212Gln	synonymous	Exon 9 of 14	ENSP00000481258.1	A0A087WXS9
	TBC1D3I	ENST00000618620.4	TSL:1	c.636G>A	p.Gln212Gln	synonymous	Exon 9 of 12	ENSP00000479474.1	A0A0B4J2F4
	TBC1D3I	ENST00000616671.4	TSL:5	c.636G>A	p.Gln212Gln	synonymous	Exon 8 of 11	ENSP00000482914.1	A0A0B4J2F4

Frequencies

GnomAD3 genomes Cov.: 3

GnomAD2 exomes AF: 0.000223 AC: 3 AN: 13456 AF XY: 0.000149

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 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

African (AFR) AF: 0.00 AC: 0 AN: 9732

American (AMR) AF: 0.00 AC: 0 AN: 14190

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5338

East Asian (EAS) AF: 0.00 AC: 0 AN: 22548

South Asian (SAS) AF: 0.00 AC: 0 AN: 30124

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 11410

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 902

European-Non Finnish (NFE) AF: 0.0000191 AC: 2 AN: 104860

Other (OTH) AF: 0.00 AC: 0 AN: 12002

GnomAD4 genome Cov.: 3

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	2.1
DANN	Benign	0.92
PhyloP100		1.1
Mutation Taster		=99/1	polymorphism

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

Other links and lift over

dbSNP: rs1271180360; hg19: chr17-34585324;