6-24559010-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_014809.4(KIAA0319):c.2734+3A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000375 in 1,608,892 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00033 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00038 ( 2 hom. )
Consequence
KIAA0319
NM_014809.4 splice_donor_region, intron
NM_014809.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.03965
2
Clinical Significance
Conservation
PhyloP100: 1.66
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 Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
Variant 6-24559010-T-C is Benign according to our data. Variant chr6-24559010-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3036021.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA0319 | NM_014809.4 | c.2734+3A>G | splice_donor_region_variant, intron_variant | ENST00000378214.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0319 | ENST00000378214.8 | c.2734+3A>G | splice_donor_region_variant, intron_variant | 1 | NM_014809.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000328 AC: 50AN: 152258Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000411 AC: 100AN: 243294Hom.: 0 AF XY: 0.000511 AC XY: 67AN XY: 131150
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GnomAD4 exome AF: 0.000380 AC: 554AN: 1456516Hom.: 2 Cov.: 30 AF XY: 0.000417 AC XY: 302AN XY: 723964
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
KIAA0319-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 30, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at