rs807532

Variant names:

• chr6-24549440-T-C
• rs807532
• NM_014809.4:c.3040+1994A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-24549440-T-C
• chr6-24549440-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.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
• Publications: 4 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.911 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.3040+1994A>G		intron	N/A	NP_055624.2
	KIAA0319	NM_001168375.2		c.3040+1994A>G		intron	N/A	NP_001161847.1
	KIAA0319	NM_001350403.2		c.3040+1994A>G		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.3040+1994A>G		intron	N/A	ENSP00000367459.3
	KIAA0319	ENST00000537886.5	TSL:1	c.2858-2097A>G		intron	N/A	ENSP00000439700.1
	KIAA0319	ENST00000616673.4	TSL:1	c.1273+1994A>G		intron	N/A	ENSP00000483665.1

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

African (AFR) AF: 0.865 AC: 35843 AN: 41444

American (AMR) AF: 0.712 AC: 10878 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3057 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2413 AN: 5142

South Asian (SAS) AF: 0.853 AC: 4100 AN: 4808

European-Finnish (FIN) AF: 0.911 AC: 9632 AN: 10576

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62383 AN: 68000

Other (OTH) AF: 0.846 AC: 1785 AN: 2110

Alfa AF: 0.892 Hom.: 250892

Bravo AF: 0.846

Asia WGS AF: 0.714 AC: 2486 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	0.062
DANN	Benign	0.33
PhyloP100		-3.9
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: rs807532; hg19: chr6-24549668;