6-24560105-C-T

Variant names:

• chr6-24560105-C-T
• rs807542
• NM_014809.4:c.2592-950G>A

Variant summary

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

The NM_014809.4(KIAA0319):​c.2592-950G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.864 in 152,064 control chromosomes in the GnomAD database, including 57,688 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 0.86 (57688 hom., cov: 34)
• Consequence: KIAA0319 NM_014809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0319	NM_014809.4	c.2592-950G>A		intron_variant	Intron 16 of 20	ENST00000378214.8	NP_055624.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA0319	ENST00000378214.8	c.2592-950G>A		intron_variant	Intron 16 of 20	1	NM_014809.4	ENSP00000367459.3

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131356 AN: 151946 Hom.: 57654 Cov.: 34

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.864 AC: 131439 AN: 152064 Hom.: 57688 Cov.: 34 AF XY: 0.858 AC XY: 63787 AN XY: 74312

African (AFR) AF: 0.867 AC: 36017 AN: 41538

American (AMR) AF: 0.716 AC: 10927 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3061 AN: 3468

East Asian (EAS) AF: 0.439 AC: 2263 AN: 5154

South Asian (SAS) AF: 0.849 AC: 4092 AN: 4818

European-Finnish (FIN) AF: 0.908 AC: 9576 AN: 10546

Middle Eastern (MID) AF: 0.870 AC: 254 AN: 292

European-Non Finnish (NFE) AF: 0.922 AC: 62633 AN: 67956

Other (OTH) AF: 0.854 AC: 1804 AN: 2112

Alfa AF: 0.899 Hom.: 7689

Bravo AF: 0.849

Asia WGS AF: 0.705 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.047
DANN	Benign	0.26
PhyloP100		-2.1
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: rs807542; hg19: chr6-24560333;