17-38058139-C-T

Variant names:

• chr17-38058139-C-T
• NM_001001418.6:c.1519G>A

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001001418.6(TBC1D3C):​c.1519G>A​(p.Ala507Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 9/12 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: TBC1D3C NM_001001418.6 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.12
• Publications: 0 publications found

Genes affected

TBC1D3C (HGNC:24889): (TBC1 domain family member 3C) This gene represents one of a cluster of related genes found on chromosome 17. The proteins encoded by this gene family contain a TBC (Tre-2, Bub2p, and Cdc16p) domain and may be involved in GTPase signaling and vesicle trafficking. [provided by RefSeq, Apr 2014]

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.029060781).
• BP6: Variant 17-38058139-C-T is Benign according to our data. Variant chr17-38058139-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2346203.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001418.6. 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
	TBC1D3C	NM_001001418.6	MANE Select	c.1519G>A	p.Ala507Thr	missense	Exon 14 of 14	NP_001001418.5	Q6IPX1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBC1D3C	ENST00000622206.2	TSL:1 MANE Select	c.1519G>A	p.Ala507Thr	missense	Exon 14 of 14	ENSP00000482345.1	Q6IPX1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 7270 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 3672

African (AFR) AF: 0.00 AC: 0 AN: 812

American (AMR) AF: 0.00 AC: 0 AN: 274

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 78

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 324

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 714

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 14

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4710

Other (OTH) AF: 0.00 AC: 0 AN: 344

GnomAD4 genome Cov.: 0

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.076
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.022
DEOGEN2	Benign	0.0033	T
Eigen	Benign	-2.3
Eigen_PC	Benign	-2.3
FATHMM_MKL	Benign	0.00024	N
M_CAP	Benign	0.00086	T
MetaRNN	Benign	0.029	T
MetaSVM	Benign	-1.0	T
PhyloP100		-4.1
Sift4G	Benign	0.64	T
Vest4		0.056
MutPred		0.11		Gain of glycosylation at A507 (P = 0.0131)
MVP		0.014
ClinPred		0.10	T
GERP RS		-0.093
gMVP		0.0013

Splicing

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

Other links and lift over

hg19: chr17-34746565;