NM_001123391.4:c.879C>T

Variant names:

• chr17-38184096-G-A
• rs1445143796
• NM_001123391.4:c.879C>T

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001123391.4(TBC1D3):​c.879C>T​(p.Gly293Gly) 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: 0)
• Consequence: TBC1D3 NM_001123391.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.61
• Publications: 0 publications found

Genes affected

TBC1D3 (HGNC:19031): (TBC1 domain family member 3) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Predicted to be located in early endosome membrane. [provided by Alliance of Genome Resources, Apr 2022]

NPEPPSP1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP6: Variant 17-38184096-G-A is Benign according to our data. Variant chr17-38184096-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2647697.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.61 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001123391.4. 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
	TBC1D3	NM_001123391.4	MANE Select	c.879C>T	p.Gly293Gly	synonymous	Exon 12 of 14	NP_001116863.3	Q8IZP1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBC1D3	ENST00000620215.3	TSL:1 MANE Select	c.879C>T	p.Gly293Gly	synonymous	Exon 12 of 14	ENSP00000478683.1	Q8IZP1-1
	TBC1D3	ENST00000896521.1		c.879C>T	p.Gly293Gly	synonymous	Exon 11 of 13	ENSP00000566580.1
	NPEPPSP1	ENST00000738688.1		n.412-29930C>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 0

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
PhyloP100		-1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1445143796; hg19: chr17-36292478;