6-24606499-G-A

Position:

• chr6-24606499-G-A

Variant summary

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

The NM_014809.4(KIAA0319):​c.-105-5291C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.913 in 152,244 control chromosomes in the GnomAD database, including 63,456 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 0.91 (63456 hom., cov: 31)
• Consequence: KIAA0319 NM_014809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0319	NM_014809.4	c.-105-5291C>T		intron_variant		ENST00000378214.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0319	ENST00000378214.8	c.-105-5291C>T		intron_variant		1	NM_014809.4	P2
KIAA0319	ENST00000537886.5	c.-105-5291C>T		intron_variant		1
KIAA0319	ENST00000430948.6	c.-80-9881C>T		intron_variant		2		A2
KIAA0319	ENST00000535378.5	c.-223-5291C>T		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138820 AN: 152126 Hom.: 63395 Cov.: 31

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.913 AC: 138940 AN: 152244 Hom.: 63456 Cov.: 31 AF XY: 0.916 AC XY: 68174 AN XY: 74450

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.936

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.908

Alfa AF: 0.901 Hom.: 26532

Bravo AF: 0.914

Asia WGS AF: 0.961 AC: 3342 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	0.81
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: rs4236032; hg19: chr6-24606727;