rs66843001

Variant names:

• chr5-894996-CAA-C
• rs66843001
• NM_004237.4:c.258+47_258+48delAA

Your query was ambiguous. Multiple possible variants found:

• chr5-894996-CAA-C
• chr5-894996-CAA-CA

Variant summary

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

The NM_004237.4(TRIP13):​c.258+47_258+48delAA variant causes a intron change involving the alteration of a non-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: 25)
• Consequence: TRIP13 NM_004237.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

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]

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
TRIP13	NM_004237.4	c.258+47_258+48delAA		intron_variant	Intron 2 of 12	ENST00000166345.8	NP_004228.1
TRIP13	NM_001166260.2	c.258+47_258+48delAA		intron_variant	Intron 2 of 8		NP_001159732.1
TRIP13	XM_011514163.2	c.258+47_258+48delAA		intron_variant	Intron 2 of 13		XP_011512465.1
TRIP13	XM_047417879.1	c.-202+47_-202+48delAA		intron_variant	Intron 2 of 12		XP_047273835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIP13	ENST00000166345.8	c.258+45_258+46delAA		intron_variant	Intron 2 of 12	1	NM_004237.4	ENSP00000166345.3
TRIP13	ENST00000512024.5	n.373+45_373+46delAA		intron_variant	Intron 2 of 8	1
TRIP13	ENST00000513435.1	c.243+45_243+46delAA		intron_variant	Intron 2 of 7	5		ENSP00000427528.1
TRIP13	ENST00000508456.1	n.232+45_232+46delAA		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes Cov.: 25

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 25

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs66843001; hg19: chr5-895111;