rs16915399

Variant names:

• chr8-92965208-T-C
• rs16915399
• ENST00000524260.1:n.281A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000524260.1(TRIQK):​n.281A>G variant causes a non coding transcript exon 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 ENST00000524260.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 1 publications found

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]

ENSG00000253577 (HGNC:58428):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRIQK	NM_001171797.2	c.-181+799A>G		intron_variant	Intron 1 of 4	ENST00000521988.6	NP_001165268.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIQK	ENST00000521988.6	c.-181+799A>G		intron_variant	Intron 1 of 4	1	NM_001171797.2	ENSP00000429517.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0556 AC: 1 AN: 18

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.00748 AC: 311 AN: 41560

American (AMR) AF: 0.00713 AC: 109 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3472

East Asian (EAS) AF: 0.0423 AC: 218 AN: 5158

South Asian (SAS) AF: 0.0706 AC: 340 AN: 4816

European-Finnish (FIN) AF: 0.0106 AC: 112 AN: 10610

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0188 AC: 1281 AN: 68006

Other (OTH) AF: 0.0147 AC: 31 AN: 2112

Alfa AF: 0.0187 Hom.: 48

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
PhyloP100		-0.50
PromoterAI		-0.025	Neutral
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: rs16915399; hg19: chr8-93977436;