rs761101

Variant names:

• chr6-24632304-G-A
• rs761101
• NM_014809.4:c.-106+13432C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-24632304-G-A
• chr6-24632304-G-C

Variant summary

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

The NM_014809.4(KIAA0319):​c.-106+13432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,134 control chromosomes in the GnomAD database, including 40,839 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 0.72 (40839 hom., cov: 32)
• Consequence: KIAA0319 NM_014809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 7 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 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.-106+13432C>T		intron	N/A	NP_055624.2	Q5VV43-1
	KIAA0319	NM_001168375.2		c.-106+13323C>T		intron	N/A	NP_001161847.1	Q5VV43-1
	KIAA0319	NM_001350403.2		c.-106+13731C>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.-106+13432C>T		intron	N/A	ENSP00000367459.3	Q5VV43-1
	KIAA0319	ENST00000537886.5	TSL:1	c.-106+13432C>T		intron	N/A	ENSP00000439700.1	Q5VV43-4
	KIAA0319	ENST00000901508.1		c.-106+13731C>T		intron	N/A	ENSP00000571567.1

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110137 AN: 152014 Hom.: 40801 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.725 AC: 110231 AN: 152134 Hom.: 40839 Cov.: 32 AF XY: 0.720 AC XY: 53558 AN XY: 74360

African (AFR) AF: 0.864 AC: 35886 AN: 41536

American (AMR) AF: 0.780 AC: 11916 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2226 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4530 AN: 5186

South Asian (SAS) AF: 0.696 AC: 3355 AN: 4822

European-Finnish (FIN) AF: 0.538 AC: 5681 AN: 10558

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44121 AN: 67974

Other (OTH) AF: 0.736 AC: 1555 AN: 2112

Alfa AF: 0.670 Hom.: 28945

Bravo AF: 0.749

Asia WGS AF: 0.794 AC: 2760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.56
PhyloP100		0.35
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: rs761101; hg19: chr6-24632532;