rs807528

Variant names:

• chr6-24544254-C-G
• rs807528
• NM_014809.4:c.*2911G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-24544254-C-G
• chr6-24544254-C-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.*2911G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,082 control chromosomes in the GnomAD database, including 5,549 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 (5549 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KIAA0319 NM_014809.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 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.*2911G>C		3_prime_UTR	Exon 21 of 21	NP_055624.2	Q5VV43-1
	KIAA0319	NM_001168375.2		c.*2911G>C		3_prime_UTR	Exon 21 of 21	NP_001161847.1	Q5VV43-1
	KIAA0319	NM_001350403.2		c.*2911G>C		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.*2911G>C		3_prime_UTR	Exon 21 of 21	ENSP00000367459.3	Q5VV43-1
	KIAA0319	ENST00000537886.5	TSL:1	c.*2911G>C		3_prime_UTR	Exon 19 of 19	ENSP00000439700.1	Q5VV43-4
	KIAA0319	ENST00000616673.4	TSL:1	c.*2911G>C		3_prime_UTR	Exon 17 of 17	ENSP00000483665.1	A0A087X0U9

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40149 AN: 151964 Hom.: 5528 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.243

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

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) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.264 AC: 40217 AN: 152082 Hom.: 5549 Cov.: 32 AF XY: 0.258 AC XY: 19207 AN XY: 74334

African (AFR) AF: 0.324 AC: 13416 AN: 41464

American (AMR) AF: 0.204 AC: 3115 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 477 AN: 3464

East Asian (EAS) AF: 0.131 AC: 678 AN: 5178

South Asian (SAS) AF: 0.266 AC: 1283 AN: 4818

European-Finnish (FIN) AF: 0.228 AC: 2409 AN: 10582

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

European-Non Finnish (NFE) AF: 0.263 AC: 17858 AN: 67986

Other (OTH) AF: 0.246 AC: 519 AN: 2110

Alfa AF: 0.145 Hom.: 276

Bravo AF: 0.265

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.48
PhyloP100		0.27
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: rs807528; hg19: chr6-24544482;