Variant chr6-24559053-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_014809.4(KIAA0319):c.2694T>C(p.Ala898=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 1,612,098 control chromosomes in the GnomAD database, including 40,425 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.19 ( 2956 hom., cov: 33)

Exomes 𝑓: 0.22 ( 37469 hom. )

Consequence

KIAA0319
NM_014809.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.72

Variant links:

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]

KIAA0319 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 6-24559053-A-G is Benign according to our data. Variant chr6-24559053-A-G is described in ClinVar as [Benign]. Clinvar id is 3060711.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-2.72 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0319	NM_014809.4 linkuse as main transcript	c.2694T>C	p.Ala898=	synonymous_variant	17/21	ENST00000378214.8	NP_055624.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA0319	ENST00000378214.8 linkuse as main transcript	c.2694T>C	p.Ala898=	synonymous_variant	17/21	1	NM_014809.4	ENSP00000367459	P2	Q5VV43-1

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

29112

AN:

152080

Hom.:

2948

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.380

Gnomad AMR

AF:

0.172

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.236

Gnomad FIN

AF:

0.205

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.184

GnomAD3 exomes

AF:

0.201

AC:

50042

AN:

248788

Hom.:

5268

AF XY:

0.204

AC XY:

27372

AN XY:

134430

show subpopulations

Gnomad AFR exome

AF:

0.143

Gnomad AMR exome

AF:

0.181

Gnomad ASJ exome

AF:

0.109

Gnomad EAS exome

AF:

0.135

Gnomad SAS exome

AF:

0.238

Gnomad FIN exome

AF:

0.210

Gnomad NFE exome

AF:

0.223

Gnomad OTH exome

AF:

0.197

GnomAD4 exome

AF:

0.223

AC:

325627

AN:

1459900

Hom.:

37469

Cov.:

AF XY:

0.223

AC XY:

161734

AN XY:

726128

show subpopulations

Gnomad4 AFR exome

AF:

0.136

Gnomad4 AMR exome

AF:

0.181

Gnomad4 ASJ exome

AF:

0.109

Gnomad4 EAS exome

AF:

0.112

Gnomad4 SAS exome

AF:

0.233

Gnomad4 FIN exome

AF:

0.213

Gnomad4 NFE exome

AF:

0.235

Gnomad4 OTH exome

AF:

0.216

GnomAD4 genome

AF:

0.191

AC:

29144

AN:

152198

Hom.:

2956

Cov.:

AF XY:

0.188

AC XY:

14012

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.143

Gnomad4 AMR

AF:

0.172

Gnomad4 ASJ

AF:

0.115

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.236

Gnomad4 FIN

AF:

0.205

Gnomad4 NFE

AF:

0.227

Gnomad4 OTH

AF:

0.189

Alfa

AF:

0.208

Hom.:

5692

Bravo

AF:

0.187

Asia WGS

AF:

0.203

AC:

709

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

KIAA0319-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 30, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

1.2

DANN

Benign

0.48

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over