rs2744564
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014809.4(KIAA0319):c.1280-35G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0322 in 1,462,394 control chromosomes in the GnomAD database, including 2,171 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 0.072 ( 935 hom., cov: 31)
Exomes 𝑓: 0.028 ( 1236 hom. )
Consequence
KIAA0319
NM_014809.4 intron
NM_014809.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.26
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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIAA0319 | NM_014809.4 | c.1280-35G>C | intron_variant | ENST00000378214.8 | NP_055624.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIAA0319 | ENST00000378214.8 | c.1280-35G>C | intron_variant | 1 | NM_014809.4 | ENSP00000367459.3 |
Frequencies
GnomAD3 genomes AF: 0.0714 AC: 10860AN: 152024Hom.: 930 Cov.: 31
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GnomAD3 exomes AF: 0.0264 AC: 4449AN: 168250Hom.: 257 AF XY: 0.0218 AC XY: 1932AN XY: 88630
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GnomAD4 exome AF: 0.0276 AC: 36176AN: 1310252Hom.: 1236 Cov.: 19 AF XY: 0.0261 AC XY: 17015AN XY: 652432
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GnomAD4 genome AF: 0.0716 AC: 10897AN: 152142Hom.: 935 Cov.: 31 AF XY: 0.0684 AC XY: 5091AN XY: 74394
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at