rs202196315

Variant names:

• chr18-31830850-G-A
• rs202196315
• NM_014939.5:c.4213C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-31830850-G-A
• chr18-31830850-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_014939.5(TRAPPC8):​c.4213C>T​(p.Pro1405Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TRAPPC8 NM_014939.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 8.92

Genes affected

TRAPPC8 (HGNC:29169): (trafficking protein particle complex subunit 8) Involved in Golgi organization. Part of TRAPP complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAPPC8	NM_014939.5	c.4213C>T	p.Pro1405Ser	missense_variant	Exon 29 of 29	ENST00000283351.10	NP_055754.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAPPC8	ENST00000283351.10	c.4213C>T	p.Pro1405Ser	missense_variant	Exon 29 of 29	1	NM_014939.5	ENSP00000283351.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.59
BayesDel_addAF	Uncertain	0.034	T
BayesDel_noAF	Benign	-0.19
CADD	Uncertain	26
DANN	Benign	0.92
DEOGEN2	Benign	0.0014	T;T
Eigen	Pathogenic	0.73
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Uncertain	0.97	D;D
M_CAP	Benign	0.038	D
MetaRNN	Uncertain	0.43	T;T
MetaSVM	Benign	-1.2	T
MutationAssessor	Uncertain	2.3	M;.
PrimateAI	Pathogenic	0.84	D
PROVEAN	Benign	-1.9	N;.
REVEL	Benign	0.24
Sift	Benign	0.050	D;.
Sift4G	Benign	0.29	T;T
Polyphen		0.99	D;.
Vest4		0.55
MutPred		0.47		Gain of catalytic residue at P1405 (P = 0.0174);.;
MVP		0.043
MPC		0.31
ClinPred		0.82	D
GERP RS		5.8
Varity_R		0.13
gMVP		0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs202196315; hg19: chr18-29410813; COSMIC: COSV51967564; COSMIC: COSV51967564;