5-894996-CA-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_004237.4(TRIP13):c.258+48del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 1,556,302 control chromosomes in the GnomAD database, including 37,006 homozygotes. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.31 (13758 hom., cov: 26)
  • Exomes 𝑓: 0.14 (23248 hom.)
• Consequence: TRIP13 NM_004237.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.00

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 -16 ACMG points.

• BP6: Variant 5-894996-CA-C is Benign according to our data. Variant chr5-894996-CA-C is described in ClinVar as [Benign]. Clinvar id is 1225568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIP13	NM_004237.4	c.258+48del		intron_variant		ENST00000166345.8
TRIP13	NM_001166260.2	c.258+48del		intron_variant
TRIP13	XM_011514163.2	c.258+48del		intron_variant
TRIP13	XM_047417879.1	c.-202+48del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIP13	ENST00000166345.8	c.258+48del		intron_variant		1	NM_004237.4	P1
TRIP13	ENST00000512024.5	n.373+48del		intron_variant, non_coding_transcript_variant		1
TRIP13	ENST00000513435.1	c.245+48del		intron_variant		5
TRIP13	ENST00000508456.1	n.232+48del		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47638 AN: 151920 Hom.: 13697 Cov.: 26

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.0984

Gnomad OTH AF: 0.264

GnomAD3 exomes AF: 0.200 AC: 41955 AN: 210044 Hom.: 7733 AF XY: 0.184 AC XY: 21019 AN XY: 114036

Gnomad AFR exome AF: 0.777

Gnomad AMR exome AF: 0.270

Gnomad ASJ exome AF: 0.139

Gnomad EAS exome AF: 0.348

Gnomad SAS exome AF: 0.220

Gnomad FIN exome AF: 0.0988

Gnomad NFE exome AF: 0.0963

Gnomad OTH exome AF: 0.159

GnomAD4 exome AF: 0.137 AC: 192097 AN: 1404264 Hom.: 23248 Cov.: 22 AF XY: 0.137 AC XY: 95051 AN XY: 695528

Gnomad4 AFR exome AF: 0.791

Gnomad4 AMR exome AF: 0.269

Gnomad4 ASJ exome AF: 0.134

Gnomad4 EAS exome AF: 0.369

Gnomad4 SAS exome AF: 0.213

Gnomad4 FIN exome AF: 0.0970

Gnomad4 NFE exome AF: 0.0997

Gnomad4 OTH exome AF: 0.176

GnomAD4 genome AF: 0.314 AC: 47766 AN: 152038 Hom.: 13758 Cov.: 26 AF XY: 0.312 AC XY: 23195 AN XY: 74332

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0984

Gnomad4 OTH AF: 0.265

Alfa AF: 0.195 Hom.: 1165

Bravo AF: 0.349

Asia WGS AF: 0.325 AC: 1131 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 26, 2019

- -

Oocyte maturation defect 9 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Mosaic variegated aneuploidy syndrome 3 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

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;