rs339408

Variant names:

• chr19-6742853-G-A
• rs339408
• NM_001288962.2:c.198-114G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRIP10	NM_001288962.2	c.198-114G>A		intron_variant	Intron 3 of 14	ENST00000313244.14	NP_001275891.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIP10	ENST00000313244.14	c.198-114G>A		intron_variant	Intron 3 of 14	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

African (AFR) AF: 0.655 AC: 18221 AN: 27828

American (AMR) AF: 0.650 AC: 18859 AN: 29016

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 12092 AN: 19400

East Asian (EAS) AF: 0.835 AC: 31826 AN: 38116

South Asian (SAS) AF: 0.620 AC: 41878 AN: 67578

European-Finnish (FIN) AF: 0.511 AC: 22320 AN: 43662

Middle Eastern (MID) AF: 0.644 AC: 2228 AN: 3462

European-Non Finnish (NFE) AF: 0.573 AC: 551481 AN: 961944

Other (OTH) AF: 0.608 AC: 31760 AN: 52210

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

African (AFR) AF: 0.652 AC: 26889 AN: 41226

American (AMR) AF: 0.641 AC: 9772 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2137 AN: 3468

East Asian (EAS) AF: 0.843 AC: 4352 AN: 5162

South Asian (SAS) AF: 0.642 AC: 3089 AN: 4812

European-Finnish (FIN) AF: 0.509 AC: 5300 AN: 10414

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39483 AN: 67976

Other (OTH) AF: 0.609 AC: 1283 AN: 2108

Alfa AF: 0.595 Hom.: 49782

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
PhyloP100		-0.70
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: rs339408; hg19: chr19-6742864;