rs16915399

chr8-92965208-T-C

Variant summary

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

The NM_001171797.2(TRIQK):c.-181+799A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0163 in 152,256 control chromosomes in the GnomAD database, including 36 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 0.016 (36 hom., cov: 32)
  • Exomes 𝑓: 0.050 (0 hom.)
• Consequence: TRIQK NM_001171797.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

Genes affected

TRIQK (HGNC:27828): (triple QxxK/R motif containing) Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIQK	NM_001171797.2	c.-181+799A>G		intron_variant		ENST00000521988.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIQK	ENST00000521988.6	c.-181+799A>G		intron_variant		1	NM_001171797.2	P1
	ENST00000523197.5	n.268-103T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0163 AC: 2480 AN: 152118 Hom.: 36 Cov.: 32

Gnomad AFR AF: 0.00753

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00707

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.0703

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.0153

GnomAD4 exome AF: 0.0500 AC: 1 AN: 20 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0556

GnomAD4 genome AF: 0.0163 AC: 2476 AN: 152236 Hom.: 36 Cov.: 32 AF XY: 0.0173 AC XY: 1285 AN XY: 74420

Gnomad4 AFR AF: 0.00748

Gnomad4 AMR AF: 0.00713

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.0423

Gnomad4 SAS AF: 0.0706

Gnomad4 FIN AF: 0.0106

Gnomad4 NFE AF: 0.0188

Gnomad4 OTH AF: 0.0147

Alfa AF: 0.0162 Hom.: 9

Bravo AF: 0.0145

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.3
Dann	Benign	0.62

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: rs16915399; hg19: chr8-93977436;