rs2817206

chr6-24620174-T-Achr6-24620174-T-C

Variant summary

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

The NM_014809.4(KIAA0319):c.-105-18966A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,216 control chromosomes in the GnomAD database, including 65,298 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 0.93 (65298 hom., cov: 31)
• Consequence: KIAA0319 NM_014809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0319	NM_014809.4	c.-105-18966A>T		intron_variant		ENST00000378214.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0319	ENST00000378214.8	c.-105-18966A>T		intron_variant		1	NM_014809.4	P2
KIAA0319	ENST00000537886.5	c.-105-18966A>T		intron_variant		1
KIAA0319	ENST00000430948.6	c.-80-23556A>T		intron_variant		2		A2
KIAA0319	ENST00000535378.5	c.-223-18966A>T		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140708 AN: 152098 Hom.: 65235 Cov.: 31

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.931

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

GnomAD4 genome AF: 0.925 AC: 140830 AN: 152216 Hom.: 65298 Cov.: 31 AF XY: 0.925 AC XY: 68842 AN XY: 74406

Gnomad4 AFR AF: 0.981

Gnomad4 AMR AF: 0.947

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.932

Alfa AF: 0.901 Hom.: 7046

Bravo AF: 0.933

Asia WGS AF: 0.971 AC: 3377 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	0.063
Dann	Benign	0.079

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: rs2817206; hg19: chr6-24620402;