6-24627975-T-C

Variant summary

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

The NM_014809.4(KIAA0319):​c.-106+17761A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,102 control chromosomes in the GnomAD database, including 38,762 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 ( 38762 hom., cov: 32)

Consequence

KIAA0319
NM_014809.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.865
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KIAA0319NM_014809.4 linkc.-106+17761A>G intron_variant ENST00000378214.8 NP_055624.2 Q5VV43-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KIAA0319ENST00000378214.8 linkc.-106+17761A>G intron_variant 1 NM_014809.4 ENSP00000367459.3 Q5VV43-1
KIAA0319ENST00000537886.5 linkc.-106+17761A>G intron_variant 1 ENSP00000439700.1 Q5VV43-4
KIAA0319ENST00000535378.5 linkc.-224+17761A>G intron_variant 2 ENSP00000442403.1 Q5VV43-2
KIAA0319ENST00000430948.6 linkc.-81+17652A>G intron_variant 2 ENSP00000401086.2 Q5VV43-3

Frequencies

GnomAD3 genomes
AF:
0.708
AC:
107570
AN:
151984
Hom.:
38725
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.811
Gnomad AMI
AF:
0.789
Gnomad AMR
AF:
0.773
Gnomad ASJ
AF:
0.636
Gnomad EAS
AF:
0.873
Gnomad SAS
AF:
0.697
Gnomad FIN
AF:
0.536
Gnomad MID
AF:
0.804
Gnomad NFE
AF:
0.647
Gnomad OTH
AF:
0.716
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.708
AC:
107661
AN:
152102
Hom.:
38762
Cov.:
32
AF XY:
0.704
AC XY:
52354
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.811
Gnomad4 AMR
AF:
0.773
Gnomad4 ASJ
AF:
0.636
Gnomad4 EAS
AF:
0.874
Gnomad4 SAS
AF:
0.694
Gnomad4 FIN
AF:
0.536
Gnomad4 NFE
AF:
0.647
Gnomad4 OTH
AF:
0.721
Alfa
AF:
0.662
Hom.:
12909
Bravo
AF:
0.730
Asia WGS
AF:
0.791
AC:
2747
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
5.4
DANN
Benign
0.74

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: rs2179515; hg19: chr6-24628203; API