rs807532

Positions:

• chr6-24549440-T-C
• chr6-24549440-T-G

Variant summary

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

The NM_014809.4(KIAA0319):​c.3040+1994A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,038 control chromosomes in the GnomAD database, including 57,400 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 (57400 hom., cov: 30)
• Consequence: KIAA0319 NM_014809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.87

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0319	NM_014809.4	c.3040+1994A>G		intron_variant		ENST00000378214.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0319	ENST00000378214.8	c.3040+1994A>G		intron_variant		1	NM_014809.4	P2

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131081 AN: 151920 Hom.: 57367 Cov.: 30

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.863 AC: 131161 AN: 152038 Hom.: 57400 Cov.: 30 AF XY: 0.857 AC XY: 63673 AN XY: 74296

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.846

Alfa AF: 0.898 Hom.: 118357

Bravo AF: 0.846

Asia WGS AF: 0.714 AC: 2486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.062
DANN	Benign	0.33

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: rs807532; hg19: chr6-24549668;