rs9922666

chr16-29687304-G-T

Variant summary

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

The NM_014298.6(QPRT):c.14-7360G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,122 control chromosomes in the GnomAD database, including 6,724 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 0.29 (6724 hom., cov: 32)
• Consequence: QPRT NM_014298.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

Genes affected

QPRT (HGNC:9755): (quinolinate phosphoribosyltransferase) This gene encodes a key enzyme in catabolism of quinolinate, an intermediate in the tryptophan-nicotinamide adenine dinucleotide pathway. Quinolinate acts as a most potent endogenous exitotoxin to neurons. Elevation of quinolinate levels in the brain has been linked to the pathogenesis of neurodegenerative disorders such as epilepsy, Alzheimer's disease, and Huntington's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
QPRT	NM_014298.6	c.14-7360G>T		intron_variant		ENST00000395384.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
QPRT	ENST00000395384.9	c.14-7360G>T		intron_variant		1	NM_014298.6	P1
QPRT	ENST00000449759.2	c.14-7360G>T		intron_variant		3		P1
QPRT	ENST00000562473.1	c.14-7360G>T		intron_variant		3
QPRT	ENST00000219771.7	n.203+8094G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43623 AN: 152004 Hom.: 6705 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.287 AC: 43677 AN: 152122 Hom.: 6724 Cov.: 32 AF XY: 0.282 AC XY: 20937 AN XY: 74374

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.250

Alfa AF: 0.263 Hom.: 5570

Bravo AF: 0.281

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.53
Dann	Benign	0.39

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: rs9922666; hg19: chr16-29698625;