Variant rs807535 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000378214.8(KIAA0319):c.2973A>G(p.Lys991=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 1,603,368 control chromosomes in the GnomAD database, including 15,042 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.12 ( 1133 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13909 hom. )

Consequence

KIAA0319
ENST00000378214.8 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.0180

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 6-24551501-T-C is Benign according to our data. Variant chr6-24551501-T-C is described in ClinVar as [Benign]. Clinvar id is 3059378.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.018 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 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.2973A>G	p.Lys991=	synonymous_variant	20/21	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.2973A>G	p.Lys991=	synonymous_variant	20/21	1	NM_014809.4	ENSP00000367459	P2	Q5VV43-1

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17925

AN:

152040

Hom.:

1132

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0956

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.0917

Gnomad ASJ

AF:

0.0793

Gnomad EAS

AF:

0.0821

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.113

GnomAD3 exomes

AF:

0.119

AC:

29890

AN:

251138

Hom.:

1897

AF XY:

0.120

AC XY:

16230

AN XY:

135746

show subpopulations

Gnomad AFR exome

AF:

0.0939

Gnomad AMR exome

AF:

0.0961

Gnomad ASJ exome

AF:

0.0740

Gnomad EAS exome

AF:

0.0904

Gnomad SAS exome

AF:

0.115

Gnomad FIN exome

AF:

0.124

Gnomad NFE exome

AF:

0.138

Gnomad OTH exome

AF:

0.119

GnomAD4 exome

AF:

0.133

AC:

193517

AN:

1451210

Hom.:

13909

Cov.:

AF XY:

0.132

AC XY:

95534

AN XY:

722520

show subpopulations

Gnomad4 AFR exome

AF:

0.0913

Gnomad4 AMR exome

AF:

0.0960

Gnomad4 ASJ exome

AF:

0.0740

Gnomad4 EAS exome

AF:

0.0595

Gnomad4 SAS exome

AF:

0.112

Gnomad4 FIN exome

AF:

0.126

Gnomad4 NFE exome

AF:

0.143

Gnomad4 OTH exome

AF:

0.132

GnomAD4 genome

AF:

0.118

AC:

17947

AN:

152158

Hom.:

1133

Cov.:

AF XY:

0.115

AC XY:

8533

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0955

Gnomad4 AMR

AF:

0.0921

Gnomad4 ASJ

AF:

0.0793

Gnomad4 EAS

AF:

0.0823

Gnomad4 SAS

AF:

0.114

Gnomad4 FIN

AF:

0.122

Gnomad4 NFE

AF:

0.142

Gnomad4 OTH

AF:

0.114

Alfa

AF:

0.127

Hom.:

1660

Bravo

AF:

0.115

Asia WGS

AF:

0.0960

AC:

336

AN:

3478

EpiCase

AF:

0.129

EpiControl

AF:

0.128

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

Dec 23, 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

-0.84

CADD

Benign

2.2

DANN

Benign

0.40

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