rs6901322

Variant names:

• chr6-24583576-T-A
• rs6901322
• NM_014809.4:c.1093+28A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-24583576-T-A
• chr6-24583576-T-C
• chr6-24583576-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014809.4(KIAA0319):​c.1093+28A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 1,473,792 control chromosomes in the GnomAD database, including 88,511 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 0.39 (13593 hom., cov: 31)
  • Exomes 𝑓: 0.32 (74918 hom.)
• Consequence: KIAA0319 NM_014809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.18
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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.1093+28A>T		intron	N/A	NP_055624.2
	KIAA0319	NM_001168375.2		c.1093+28A>T		intron	N/A	NP_001161847.1
	KIAA0319	NM_001350403.2		c.1093+28A>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.1093+28A>T		intron	N/A	ENSP00000367459.3
	KIAA0319	ENST00000537886.5	TSL:1	c.1093+28A>T		intron	N/A	ENSP00000439700.1
	KIAA0319	ENST00000535378.5	TSL:2	c.1066+28A>T		intron	N/A	ENSP00000442403.1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59867 AN: 151800 Hom.: 13571 Cov.: 31

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.390

GnomAD2 exomes AF: 0.381 AC: 91955 AN: 241568 AF XY: 0.367

Gnomad AFR exome AF: 0.576

Gnomad AMR exome AF: 0.559

Gnomad ASJ exome AF: 0.309

Gnomad EAS exome AF: 0.773

Gnomad FIN exome AF: 0.237

Gnomad NFE exome AF: 0.277

Gnomad OTH exome AF: 0.330

GnomAD4 exome AF: 0.319 AC: 421319 AN: 1321874 Hom.: 74918 Cov.: 19 AF XY: 0.318 AC XY: 210974 AN XY: 664402

African (AFR) AF: 0.584 AC: 17630 AN: 30200

American (AMR) AF: 0.547 AC: 22537 AN: 41234

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 7786 AN: 24996

East Asian (EAS) AF: 0.737 AC: 28691 AN: 38916

South Asian (SAS) AF: 0.378 AC: 30839 AN: 81562

European-Finnish (FIN) AF: 0.239 AC: 12732 AN: 53274

Middle Eastern (MID) AF: 0.286 AC: 1561 AN: 5452

European-Non Finnish (NFE) AF: 0.283 AC: 280049 AN: 990470

Other (OTH) AF: 0.350 AC: 19494 AN: 55770

GnomAD4 genome AF: 0.395 AC: 59934 AN: 151918 Hom.: 13593 Cov.: 31 AF XY: 0.394 AC XY: 29268 AN XY: 74238

African (AFR) AF: 0.563 AC: 23309 AN: 41394

American (AMR) AF: 0.473 AC: 7229 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1147 AN: 3468

East Asian (EAS) AF: 0.754 AC: 3891 AN: 5160

South Asian (SAS) AF: 0.413 AC: 1988 AN: 4814

European-Finnish (FIN) AF: 0.229 AC: 2417 AN: 10552

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18759 AN: 67936

Other (OTH) AF: 0.397 AC: 839 AN: 2114

Alfa AF: 0.325 Hom.: 1704

Bravo AF: 0.424

Asia WGS AF: 0.574 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.56
PhyloP100		-5.2
PromoterAI		-0.011	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs6901322; hg19: chr6-24583804; COSMIC: COSV107486686; COSMIC: COSV107486686;