rs2817241

Variant names:

• chr6-24542035-G-A
• rs2817241
• ENST00000827594.1:n.47-690C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000827594.1(ENSG00000307634):​n.47-690C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,116 control chromosomes in the GnomAD database, including 13,716 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 0.41 (13716 hom., cov: 33)
• Consequence: ENSG00000307634 ENST00000827594.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 2 publications found

Genes affected

ENSG00000307634 (HGNC:):

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0319	XM_047419602.1	c.3041-690C>T		intron_variant	Intron 20 of 20		XP_047275558.1
KIAA0319	XM_017011546.3	c.2858-690C>T		intron_variant	Intron 18 of 18		XP_016867035.1
KIAA0319	XM_017011550.2	c.*13-690C>T		intron_variant	Intron 19 of 19		XP_016867039.1
KIAA0319	XM_047419604.1	c.*13-690C>T		intron_variant	Intron 18 of 18		XP_047275560.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307634	ENST00000827594.1	n.47-690C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61802 AN: 151996 Hom.: 13723 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.405

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.406 AC: 61788 AN: 152116 Hom.: 13716 Cov.: 33 AF XY: 0.407 AC XY: 30282 AN XY: 74358

African (AFR) AF: 0.244 AC: 10150 AN: 41522

American (AMR) AF: 0.371 AC: 5680 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1871 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1193 AN: 5166

South Asian (SAS) AF: 0.368 AC: 1774 AN: 4822

European-Finnish (FIN) AF: 0.559 AC: 5897 AN: 10556

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33938 AN: 67972

Other (OTH) AF: 0.404 AC: 852 AN: 2108

Alfa AF: 0.448 Hom.: 2106

Bravo AF: 0.385

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.83
PhyloP100		0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2817241; hg19: chr6-24542263;