rs5026394

chr6-24590319-A-C

Variant summary

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

The NM_014809.4(KIAA0319):c.802-1534T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 150,552 control chromosomes in the GnomAD database, including 11,715 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 0.39 (11715 hom., cov: 30)
• Consequence: KIAA0319 NM_014809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

KIAA0319 (HGNC:21580): (KIAA0319) This gene encodes a transmembrane protein that contains a large extracellular domain with multiple polycystic kidney disease (PKD) domains. The encoded protein may play a role in the development of the cerebral cortex by regulating neuronal migration and cell adhesion. Single nucleotide polymorphisms in this gene are associated with dyslexia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0319	NM_014809.4	c.802-1534T>G		intron_variant		ENST00000378214.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0319	ENST00000378214.8	c.802-1534T>G		intron_variant		1	NM_014809.4	P2
KIAA0319	ENST00000537886.5	c.802-1534T>G		intron_variant		1
KIAA0319	ENST00000430948.6	c.667-1534T>G		intron_variant		2		A2
KIAA0319	ENST00000535378.5	c.775-1534T>G		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59075 AN: 150448 Hom.: 11698 Cov.: 30

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.413

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.393 AC: 59117 AN: 150552 Hom.: 11715 Cov.: 30 AF XY: 0.391 AC XY: 28742 AN XY: 73472

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.391

Alfa AF: 0.401 Hom.: 24476

Bravo AF: 0.399

Asia WGS AF: 0.416 AC: 1418 AN: 3412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.5
Dann	Benign	0.24

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: rs5026394; hg19: chr6-24590547;