7-100873422-C-T

Variant names:

• chr7-100873422-C-T
• rs6706
• NM_003302.3:c.*119C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003302.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIP6	NM_003302.3	MANE Select	c.*119C>T		3_prime_UTR	Exon 9 of 9	NP_003293.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIP6	ENST00000200457.9	TSL:1 MANE Select	c.*119C>T		3_prime_UTR	Exon 9 of 9	ENSP00000200457.4
	TRIP6	ENST00000476870.5	TSL:2	n.1719C>T		non_coding_transcript_exon	Exon 8 of 8
	TRIP6	ENST00000619988.4	TSL:1	c.*1179C>T		downstream_gene	N/A	ENSP00000479865.1

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

African (AFR) AF: 0.0475 AC: 1335 AN: 28124

American (AMR) AF: 0.120 AC: 3264 AN: 27248

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 4060 AN: 19014

East Asian (EAS) AF: 0.0261 AC: 946 AN: 36292

South Asian (SAS) AF: 0.125 AC: 7756 AN: 61972

European-Finnish (FIN) AF: 0.216 AC: 7517 AN: 34868

Middle Eastern (MID) AF: 0.191 AC: 696 AN: 3640

European-Non Finnish (NFE) AF: 0.182 AC: 179485 AN: 985040

Other (OTH) AF: 0.161 AC: 8369 AN: 52104

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

African (AFR) AF: 0.0508 AC: 2113 AN: 41564

American (AMR) AF: 0.107 AC: 1630 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3470

East Asian (EAS) AF: 0.0326 AC: 169 AN: 5182

South Asian (SAS) AF: 0.113 AC: 544 AN: 4830

European-Finnish (FIN) AF: 0.211 AC: 2240 AN: 10594

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12377 AN: 68008

Other (OTH) AF: 0.139 AC: 293 AN: 2112

Alfa AF: 0.162 Hom.: 2811

Bravo AF: 0.123

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	9.6
DANN	Benign	0.77
PhyloP100		0.78
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6706; hg19: chr7-100471044;