rs2817200

Variant names:

• chr6-24584138-A-G
• rs2817200
• NM_014809.4:c.995-436T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-24584138-A-G
• chr6-24584138-A-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.995-436T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,930 control chromosomes in the GnomAD database, including 9,583 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 0.35 (9583 hom., cov: 30)
• Consequence: KIAA0319 NM_014809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 13 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0319	NM_014809.4	MANE Select	c.995-436T>C		intron	N/A	NP_055624.2	Q5VV43-1
	KIAA0319	NM_001168375.2		c.995-436T>C		intron	N/A	NP_001161847.1	Q5VV43-1
	KIAA0319	NM_001350403.2		c.995-436T>C		intron	N/A	NP_001337332.1	Q5VV43-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0319	ENST00000378214.8	TSL:1 MANE Select	c.995-436T>C		intron	N/A	ENSP00000367459.3	Q5VV43-1
	KIAA0319	ENST00000537886.5	TSL:1	c.995-436T>C		intron	N/A	ENSP00000439700.1	Q5VV43-4
	KIAA0319	ENST00000901508.1		c.995-436T>C		intron	N/A	ENSP00000571567.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52748 AN: 151812 Hom.: 9577 Cov.: 30

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.347 AC: 52783 AN: 151930 Hom.: 9583 Cov.: 30 AF XY: 0.352 AC XY: 26151 AN XY: 74250

African (AFR) AF: 0.273 AC: 11304 AN: 41434

American (AMR) AF: 0.309 AC: 4710 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1287 AN: 3464

East Asian (EAS) AF: 0.256 AC: 1325 AN: 5172

South Asian (SAS) AF: 0.299 AC: 1440 AN: 4824

European-Finnish (FIN) AF: 0.487 AC: 5119 AN: 10520

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26620 AN: 67944

Other (OTH) AF: 0.326 AC: 687 AN: 2106

Alfa AF: 0.369 Hom.: 22615

Bravo AF: 0.333

Asia WGS AF: 0.263 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.84
PhyloP100		-0.23
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: rs2817200; hg19: chr6-24584366;