5-896867-C-CG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_004237.4(TRIP13):c.388+73_388+74insG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00288 in 1,481,258 control chromosomes in the GnomAD database, including 97 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.015 (55 hom., cov: 32)
  • Exomes 𝑓: 0.0014 (42 hom.)
• Consequence: TRIP13 NM_004237.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.74

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 Benign. Variant got -10 ACMG points.

• BP6: Variant 5-896867-C-CG is Benign according to our data. Variant chr5-896867-C-CG is described in ClinVar as [Benign]. Clinvar id is 1269357.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIP13	NM_004237.4	c.388+73_388+74insG		intron_variant		ENST00000166345.8
TRIP13	NM_001166260.2	c.388+73_388+74insG		intron_variant
TRIP13	XM_011514163.2	c.388+73_388+74insG		intron_variant
TRIP13	XM_047417879.1	c.-72+73_-72+74insG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIP13	ENST00000166345.8	c.388+73_388+74insG		intron_variant		1	NM_004237.4	P1
TRIP13	ENST00000512024.5	n.503+73_503+74insG		intron_variant, non_coding_transcript_variant		1
TRIP13	ENST00000513435.1	c.375+73_375+74insG		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0154 AC: 2340 AN: 151776 Hom.: 55 Cov.: 32

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00590

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000368

Gnomad OTH AF: 0.0134

GnomAD4 exome AF: 0.00144 AC: 1918 AN: 1329364 Hom.: 42 AF XY: 0.00131 AC XY: 859 AN XY: 654264

Gnomad4 AFR exome AF: 0.0461

Gnomad4 AMR exome AF: 0.00303

Gnomad4 ASJ exome AF: 0.0000904

Gnomad4 EAS exome AF: 0.0000274

Gnomad4 SAS exome AF: 0.000382

Gnomad4 FIN exome AF: 0.0000207

Gnomad4 NFE exome AF: 0.000242

Gnomad4 OTH exome AF: 0.00402

GnomAD4 genome AF: 0.0154 AC: 2342 AN: 151894 Hom.: 55 Cov.: 32 AF XY: 0.0136 AC XY: 1009 AN XY: 74248

Gnomad4 AFR AF: 0.0532

Gnomad4 AMR AF: 0.00589

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000368

Gnomad4 OTH AF: 0.0133

Alfa AF: 0.000168 Hom.: 0

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 27, 2019

- -

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: rs369578570; hg19: chr5-896982;