7-100873422-C-T

Position:

• chr7-100873422-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003302.3(TRIP6):​c.*119C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 1,400,566 control chromosomes in the GnomAD database, including 21,228 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.13 (1714 hom., cov: 32)
  • Exomes 𝑓: 0.17 (19514 hom.)
• Consequence: TRIP6 NM_003302.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.784

Genes affected

TRIP6 (HGNC:12311): (thyroid hormone receptor interactor 6) This gene is a member of the zyxin family and encodes a protein with three LIM zinc-binding domains. This protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner and it regulates LPA-induced cell migration. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

TRIP6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIP6	NM_003302.3	c.*119C>T		3_prime_UTR_variant	9/9	ENST00000200457.9	NP_003293.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIP6	ENST00000200457.9	c.*119C>T		3_prime_UTR_variant	9/9	1	NM_003302.3	ENSP00000200457.4
TRIP6	ENST00000476870.5	n.1719C>T		non_coding_transcript_exon_variant	8/8	2

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20327 AN: 152146 Hom.: 1719 Cov.: 32

Gnomad AFR AF: 0.0508

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.139

GnomAD4 exome AF: 0.171 AC: 213428 AN: 1248302 Hom.: 19514 Cov.: 17 AF XY: 0.170 AC XY: 104049 AN XY: 611924

Gnomad4 AFR exome AF: 0.0475

Gnomad4 AMR exome AF: 0.120

Gnomad4 ASJ exome AF: 0.214

Gnomad4 EAS exome AF: 0.0261

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.216

Gnomad4 NFE exome AF: 0.182

Gnomad4 OTH exome AF: 0.161

GnomAD4 genome AF: 0.133 AC: 20321 AN: 152264 Hom.: 1714 Cov.: 32 AF XY: 0.132 AC XY: 9827 AN XY: 74448

Gnomad4 AFR AF: 0.0508

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0326

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.139

Alfa AF: 0.167 Hom.: 2296

Bravo AF: 0.123

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	9.6
DANN	Benign	0.77
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs6706; hg19: chr7-100471044;