chr6-24590319-A-C

Variant names:

• chr6-24590319-A-C
• rs5026394
• NM_014809.4:c.802-1534T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014809.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0319	NM_014809.4	MANE Select	c.802-1534T>G		intron	N/A	NP_055624.2
	KIAA0319	NM_001168375.2		c.802-1534T>G		intron	N/A	NP_001161847.1
	KIAA0319	NM_001350403.2		c.802-1534T>G		intron	N/A	NP_001337332.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0319	ENST00000378214.8	TSL:1 MANE Select	c.802-1534T>G		intron	N/A	ENSP00000367459.3
	KIAA0319	ENST00000537886.5	TSL:1	c.802-1534T>G		intron	N/A	ENSP00000439700.1
	KIAA0319	ENST00000535378.5	TSL:2	c.775-1534T>G		intron	N/A	ENSP00000442403.1

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

African (AFR) AF: 0.380 AC: 15592 AN: 40988

American (AMR) AF: 0.404 AC: 6111 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1385 AN: 3460

East Asian (EAS) AF: 0.396 AC: 2036 AN: 5144

South Asian (SAS) AF: 0.450 AC: 2152 AN: 4780

European-Finnish (FIN) AF: 0.371 AC: 3745 AN: 10100

Middle Eastern (MID) AF: 0.403 AC: 117 AN: 290

European-Non Finnish (NFE) AF: 0.394 AC: 26676 AN: 67646

Other (OTH) AF: 0.391 AC: 818 AN: 2094

Alfa AF: 0.400 Hom.: 51800

Bravo AF: 0.399

Asia WGS AF: 0.416 AC: 1418 AN: 3412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.24
PhyloP100		1.1
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: rs5026394; hg19: chr6-24590547;