rs339408

Positions:

• chr19-6742853-G-A
• chr19-6742853-G-T

Variant summary

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

The NM_001288962.2(TRIP10):​c.198-114G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 1,394,828 control chromosomes in the GnomAD database, including 246,047 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 0.61 (28931 hom., cov: 30)
  • Exomes 𝑓: 0.59 (217116 hom.)
• Consequence: TRIP10 NM_001288962.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

Genes affected

TRIP10 (HGNC:12304): (thyroid hormone receptor interactor 10) Enables identical protein binding activity. Predicted to be involved in actin cytoskeleton organization; endocytosis; and signal transduction. Located in nucleoplasm. Biomarker of Huntington's disease. [provided by Alliance of Genome Resources, Apr 2022]

TRIP10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIP10	NM_001288962.2	c.198-114G>A		intron_variant		ENST00000313244.14	NP_001275891.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIP10	ENST00000313244.14	c.198-114G>A		intron_variant		1	NM_001288962.2	ENSP00000320117.7

Frequencies

GnomAD3 genomes AF: 0.614 AC: 92993 AN: 151494 Hom.: 28911 Cov.: 30

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.607

GnomAD4 exome AF: 0.588 AC: 730665 AN: 1243216 Hom.: 217116 AF XY: 0.588 AC XY: 361553 AN XY: 614428

Gnomad4 AFR exome AF: 0.655

Gnomad4 AMR exome AF: 0.650

Gnomad4 ASJ exome AF: 0.623

Gnomad4 EAS exome AF: 0.835

Gnomad4 SAS exome AF: 0.620

Gnomad4 FIN exome AF: 0.511

Gnomad4 NFE exome AF: 0.573

Gnomad4 OTH exome AF: 0.608

GnomAD4 genome AF: 0.614 AC: 93061 AN: 151612 Hom.: 28931 Cov.: 30 AF XY: 0.612 AC XY: 45274 AN XY: 74014

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.609

Alfa AF: 0.590 Hom.: 34994

Bravo AF: 0.627

Asia WGS AF: 0.698 AC: 2428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.45

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: rs339408; hg19: chr19-6742864;