chr6-24544675-G-A

Variant names:

• chr6-24544675-G-A
• rs699463
• NM_014809.4:c.*2490C>T

Variant summary

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

The NM_014809.4(KIAA0319):​c.*2490C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,044 control chromosomes in the GnomAD database, including 5,518 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 0.26 (5517 hom., cov: 32)
  • Exomes 𝑓: 0.19 (1 hom.)
• Consequence: KIAA0319 NM_014809.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986
• Publications: 10 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014809.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0319	NM_014809.4	MANE Select	c.*2490C>T		3_prime_UTR	Exon 21 of 21	NP_055624.2	Q5VV43-1
	KIAA0319	NM_001168375.2		c.*2490C>T		3_prime_UTR	Exon 21 of 21	NP_001161847.1	Q5VV43-1
	KIAA0319	NM_001350403.2		c.*2490C>T		3_prime_UTR	Exon 21 of 21	NP_001337332.1	Q5VV43-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA0319	ENST00000378214.8	TSL:1 MANE Select	c.*2490C>T		3_prime_UTR	Exon 21 of 21	ENSP00000367459.3	Q5VV43-1
	KIAA0319	ENST00000537886.5	TSL:1	c.*2490C>T		3_prime_UTR	Exon 19 of 19	ENSP00000439700.1	Q5VV43-4
	KIAA0319	ENST00000616673.4	TSL:1	c.*2490C>T		3_prime_UTR	Exon 17 of 17	ENSP00000483665.1	A0A087X0U9

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39970 AN: 151908 Hom.: 5496 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.240

GnomAD4 exome AF: 0.188 AC: 3 AN: 16 Hom.: 1 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.214 AC: 3 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.263 AC: 40038 AN: 152028 Hom.: 5517 Cov.: 32 AF XY: 0.258 AC XY: 19161 AN XY: 74328

African (AFR) AF: 0.323 AC: 13387 AN: 41458

American (AMR) AF: 0.197 AC: 3005 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3468

East Asian (EAS) AF: 0.130 AC: 673 AN: 5168

South Asian (SAS) AF: 0.266 AC: 1283 AN: 4816

European-Finnish (FIN) AF: 0.228 AC: 2411 AN: 10564

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17827 AN: 67968

Other (OTH) AF: 0.244 AC: 512 AN: 2102

Alfa AF: 0.258 Hom.: 22660

Bravo AF: 0.263

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.32
DANN	Benign	0.70
PhyloP100		-0.99
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs699463; hg19: chr6-24544903;