rs6901592

Variant names:

• chr6-163448941-G-A
• rs6901592
• NM_006775.3:c.143-6338G>A

Variant summary

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

The NM_006775.3(QKI):​c.143-6338G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 152,034 control chromosomes in the GnomAD database, including 531 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 0.079 (531 hom., cov: 31)
• Consequence: QKI NM_006775.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 3 publications found

Genes affected

QKI (HGNC:21100): (QKI, KH domain containing RNA binding) The protein encoded by this gene is an RNA-binding protein that regulates pre-mRNA splicing, export of mRNAs from the nucleus, protein translation, and mRNA stability. The encoded protein is involved in myelinization and oligodendrocyte differentiation and may play a role in schizophrenia. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
QKI	NM_006775.3	c.143-6338G>A		intron_variant	Intron 1 of 7	ENST00000361752.8	NP_006766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
QKI	ENST00000361752.8	c.143-6338G>A		intron_variant	Intron 1 of 7	1	NM_006775.3	ENSP00000355094.3

Frequencies

GnomAD3 genomes AF: 0.0788 AC: 11964 AN: 151916 Hom.: 531 Cov.: 31

Gnomad AFR AF: 0.0987

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0889

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0618

Gnomad FIN AF: 0.0418

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0787 AC: 11965 AN: 152034 Hom.: 531 Cov.: 31 AF XY: 0.0768 AC XY: 5703 AN XY: 74296

African (AFR) AF: 0.0986 AC: 4086 AN: 41442

American (AMR) AF: 0.0687 AC: 1050 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0889 AC: 308 AN: 3466

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0616 AC: 297 AN: 4820

European-Finnish (FIN) AF: 0.0418 AC: 441 AN: 10546

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0803 AC: 5458 AN: 67986

Other (OTH) AF: 0.0783 AC: 165 AN: 2108

Alfa AF: 0.0811 Hom.: 99

Bravo AF: 0.0810

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.41
PhyloP100		-0.41
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: rs6901592; hg19: chr6-163869973;