rs1035833

Positions:

• chr2-229844482-A-G

Variant summary

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

The NM_001348323.3(TRIP12):​c.1028-3555T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,150 control chromosomes in the GnomAD database, including 5,689 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 0.26 (5689 hom., cov: 32)
• Consequence: TRIP12 NM_001348323.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

Genes affected

TRIP12 (HGNC:12306): (thyroid hormone receptor interactor 12) The protein encoded by this gene is an E3 ubiquitin-protein ligase involved in the degradation of the p19ARF/ARF isoform of CDKN2A, a tumor suppressor. The encoded protein also plays a role in the DNA damage response by regulating the stability of USP7, which regulates tumor suppressor p53. [provided by RefSeq, Jan 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIP12	NM_001348323.3	c.1028-3555T>C		intron_variant		ENST00000675903.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIP12	ENST00000675903.1	c.1028-3555T>C		intron_variant			NM_001348323.3	P3

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38917 AN: 152032 Hom.: 5690 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.256 AC: 38916 AN: 152150 Hom.: 5689 Cov.: 32 AF XY: 0.265 AC XY: 19722 AN XY: 74376

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.275

Alfa AF: 0.286 Hom.: 3293

Bravo AF: 0.245

Asia WGS AF: 0.339 AC: 1175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.56
DANN	Benign	0.82

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: rs1035833; hg19: chr2-230709198;