chr6-24544247-T-C

Position:

• chr6-24544247-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014809.4(KIAA0319):​c.*2918A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,170 control chromosomes in the GnomAD database, including 58,384 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 0.87 (58384 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: KIAA0319 NM_014809.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0319	NM_014809.4	c.*2918A>G		3_prime_UTR_variant	21/21	ENST00000378214.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0319	ENST00000378214.8	c.*2918A>G		3_prime_UTR_variant	21/21	1	NM_014809.4	P2

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132266 AN: 152052 Hom.: 58350 Cov.: 32

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.857

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.870 AC: 132347 AN: 152170 Hom.: 58384 Cov.: 32 AF XY: 0.863 AC XY: 64220 AN XY: 74390

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.883

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.929

Gnomad4 OTH AF: 0.857

Alfa AF: 0.904 Hom.: 54772

Bravo AF: 0.853

Asia WGS AF: 0.717 AC: 2496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.57
DANN	Benign	0.39

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

Other links and lift over

dbSNP: rs807527; hg19: chr6-24544475;