5-894938-G-T

Position:

• chr5-894938-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004237.4(TRIP13):​c.244G>T​(p.Val82Phe) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TRIP13 NM_004237.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

TRIP13 (HGNC:12307): (thyroid hormone receptor interactor 13) This gene encodes a protein that interacts with thyroid hormone receptors, also known as hormone-dependent transcription factors. The gene product interacts specifically with the ligand binding domain. This gene is one of several that may play a role in early-stage non-small cell lung cancer. [provided by RefSeq, Oct 2009]

TRIP13 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06029451).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIP13	NM_004237.4	c.244G>T	p.Val82Phe	missense_variant	2/13	ENST00000166345.8	NP_004228.1
TRIP13	NM_001166260.2	c.244G>T	p.Val82Phe	missense_variant	2/9		NP_001159732.1
TRIP13	XM_011514163.2	c.244G>T	p.Val82Phe	missense_variant	2/14		XP_011512465.1
TRIP13	XM_047417879.1	c.-216G>T		5_prime_UTR_variant	2/13		XP_047273835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIP13	ENST00000166345.8	c.244G>T	p.Val82Phe	missense_variant	2/13	1	NM_004237.4	ENSP00000166345.3
TRIP13	ENST00000512024.5	n.359G>T		non_coding_transcript_exon_variant	2/9	1
TRIP13	ENST00000513435.1	c.229G>T	p.Val77Phe	missense_variant	2/8	5		ENSP00000427528.1
TRIP13	ENST00000508456.1	n.218G>T		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

Alfa AF: 0.0000216 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.085
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	11
DANN	Benign	0.96
DEOGEN2	Benign	0.15	T
Eigen	Benign	-0.76
Eigen_PC	Benign	-0.73
FATHMM_MKL	Benign	0.13	N
LIST_S2	Benign	0.82	T
M_CAP	Benign	0.0017	T
MetaRNN	Benign	0.060	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.81	L
PrimateAI	Benign	0.41	T
PROVEAN	Benign	-1.0	N
REVEL	Benign	0.090
Sift	Benign	0.50	T
Sift4G	Benign	0.65	T
Polyphen		0.010	B
Vest4		0.14
MutPred		0.27		Gain of loop (P = 0.069);
MVP		0.50
MPC		0.78
ClinPred		0.025	T
GERP RS		2.2
Varity_R		0.033
gMVP		0.34

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

Publications

LitVar

Other links and lift over

dbSNP: rs1804865; hg19: chr5-895053;