rs4352670

Variant names:

• chr6-24603840-C-A
• rs4352670
• NM_014809.4:c.-105-2632G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-24603840-C-A
• chr6-24603840-C-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.-105-2632G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.912 in 152,222 control chromosomes in the GnomAD database, including 63,421 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 0.91 (63421 hom., cov: 31)
• Consequence: KIAA0319 NM_014809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 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.-105-2632G>T		intron	N/A	NP_055624.2	Q5VV43-1
	KIAA0319	NM_001168375.2		c.-105-2632G>T		intron	N/A	NP_001161847.1	Q5VV43-1
	KIAA0319	NM_001350403.2		c.-105-2632G>T		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.-105-2632G>T		intron	N/A	ENSP00000367459.3	Q5VV43-1
	KIAA0319	ENST00000537886.5	TSL:1	c.-105-2632G>T		intron	N/A	ENSP00000439700.1	Q5VV43-4
	KIAA0319	ENST00000901508.1		c.-105-2632G>T		intron	N/A	ENSP00000571567.1

Frequencies

GnomAD3 genomes AF: 0.912 AC: 138774 AN: 152104 Hom.: 63361 Cov.: 31

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.912 AC: 138893 AN: 152222 Hom.: 63421 Cov.: 31 AF XY: 0.915 AC XY: 68126 AN XY: 74416

African (AFR) AF: 0.923 AC: 38352 AN: 41534

American (AMR) AF: 0.936 AC: 14307 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3185 AN: 3472

East Asian (EAS) AF: 0.984 AC: 5085 AN: 5166

South Asian (SAS) AF: 0.936 AC: 4510 AN: 4818

European-Finnish (FIN) AF: 0.919 AC: 9753 AN: 10614

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.894 AC: 60823 AN: 68004

Other (OTH) AF: 0.908 AC: 1921 AN: 2116

Alfa AF: 0.903 Hom.: 9170

Bravo AF: 0.914

Asia WGS AF: 0.961 AC: 3342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.43
PhyloP100		0.43
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: rs4352670; hg19: chr6-24604068;