rs2745333

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000378214.8(KIAA0319):​c.-105-16761T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 151,894 control chromosomes in the GnomAD database, including 39,601 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 0.71 ( 39601 hom., cov: 30)

Consequence

KIAA0319
ENST00000378214.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.585
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KIAA0319NM_014809.4 linkuse as main transcriptc.-105-16761T>C intron_variant ENST00000378214.8 NP_055624.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KIAA0319ENST00000378214.8 linkuse as main transcriptc.-105-16761T>C intron_variant 1 NM_014809.4 ENSP00000367459 P2Q5VV43-1
KIAA0319ENST00000537886.5 linkuse as main transcriptc.-105-16761T>C intron_variant 1 ENSP00000439700 Q5VV43-4
KIAA0319ENST00000430948.6 linkuse as main transcriptc.-80-21351T>C intron_variant 2 ENSP00000401086 A2Q5VV43-3
KIAA0319ENST00000535378.5 linkuse as main transcriptc.-223-16761T>C intron_variant 2 ENSP00000442403 A2Q5VV43-2

Frequencies

GnomAD3 genomes
AF:
0.705
AC:
107004
AN:
151776
Hom.:
39546
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.915
Gnomad AMI
AF:
0.748
Gnomad AMR
AF:
0.754
Gnomad ASJ
AF:
0.626
Gnomad EAS
AF:
0.878
Gnomad SAS
AF:
0.742
Gnomad FIN
AF:
0.480
Gnomad MID
AF:
0.758
Gnomad NFE
AF:
0.588
Gnomad OTH
AF:
0.723
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.705
AC:
107115
AN:
151894
Hom.:
39601
Cov.:
30
AF XY:
0.701
AC XY:
52020
AN XY:
74238
show subpopulations
Gnomad4 AFR
AF:
0.915
Gnomad4 AMR
AF:
0.754
Gnomad4 ASJ
AF:
0.626
Gnomad4 EAS
AF:
0.879
Gnomad4 SAS
AF:
0.740
Gnomad4 FIN
AF:
0.480
Gnomad4 NFE
AF:
0.588
Gnomad4 OTH
AF:
0.728
Alfa
AF:
0.643
Hom.:
4019
Bravo
AF:
0.737
Asia WGS
AF:
0.811
AC:
2821
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.52
DANN
Benign
0.28

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.

Other links and lift over

dbSNP: rs2745333; hg19: chr6-24618197; API