6-24620174-T-A

Variant names:

• chr6-24620174-T-A
• rs2817206
• NM_014809.4:c.-105-18966A>T

Variant summary

Our verdict is Benign. The variant received -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
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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.-105-18966A>T		intron	N/A	NP_055624.2
	KIAA0319	NM_001168375.2		c.-105-18966A>T		intron	N/A	NP_001161847.1
	KIAA0319	NM_001350403.2		c.-105-18966A>T		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.-105-18966A>T		intron	N/A	ENSP00000367459.3
	KIAA0319	ENST00000537886.5	TSL:1	c.-105-18966A>T		intron	N/A	ENSP00000439700.1
	KIAA0319	ENST00000535378.5	TSL:2	c.-223-18966A>T		intron	N/A	ENSP00000442403.1

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

African (AFR) AF: 0.981 AC: 40773 AN: 41546

American (AMR) AF: 0.947 AC: 14479 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3126 AN: 3472

East Asian (EAS) AF: 0.986 AC: 5103 AN: 5178

South Asian (SAS) AF: 0.961 AC: 4630 AN: 4818

European-Finnish (FIN) AF: 0.873 AC: 9234 AN: 10580

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60413 AN: 68022

Other (OTH) AF: 0.932 AC: 1965 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.063
DANN	Benign	0.079
PhyloP100		-1.3
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: rs2817206; hg19: chr6-24620402;