NM_015351.2:c.308C>T

Variant names:

• chr14-70642437-C-T
• rs1321690062
• NM_015351.2:c.308C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_015351.2(TTC9):​c.308C>T​(p.Pro103Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: TTC9 NM_015351.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.02
• Publications: 0 publications found

Genes affected

TTC9 (HGNC:20267): (tetratricopeptide repeat domain 9) This gene encodes a protein that contains three tetratricopeptide repeats. The gene has been shown to be hormonally regulated in breast cancer cells and may play a role in cancer cell invasion and metastasis. [provided by RefSeq, Mar 2009]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.113170624).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015351.2. 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
	TTC9	NM_015351.2	MANE Select	c.308C>T	p.Pro103Leu	missense	Exon 1 of 3	NP_056166.1	Q92623

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC9	ENST00000256367.3	TSL:1 MANE Select	c.308C>T	p.Pro103Leu	missense	Exon 1 of 3	ENSP00000256367.2	Q92623
	TTC9	ENST00000928641.1		c.308C>T	p.Pro103Leu	missense	Exon 1 of 2	ENSP00000598700.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 40

GnomAD4 genome Cov.: 31

ClinVar

ClinVar submissions

Significance: Uncertain significance

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	0.078
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	18
DANN	Benign	0.86
DEOGEN2	Benign	0.0015	T
Eigen	Benign	-0.41
Eigen_PC	Benign	-0.40
FATHMM_MKL	Benign	0.64	D
LIST_S2	Benign	0.27	T
M_CAP	Benign	0.013	T
MetaRNN	Benign	0.11	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.77	N
PhyloP100		3.0
PrimateAI	Uncertain	0.73	T
PROVEAN	Benign	-0.30	N
REVEL	Benign	0.036
Sift	Benign	0.24	T
Sift4G	Benign	0.32	T
Polyphen		0.76	P
Vest4		0.072
MutPred		0.24		Gain of catalytic residue at A107 (P = 0.0504)
MVP		0.22
MPC		0.64
ClinPred		0.26	T
GERP RS		3.4
Varity_R		0.061
gMVP		0.21
Mutation Taster		=98/2	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs1321690062; hg19: chr14-71109154; COSMIC: COSV56448610; COSMIC: COSV56448610;