XM_047419602.1:c.*931A>G

Variant names:

• chr6-24540311-T-C
• rs2744604
• XM_047419602.1:c.*931A>G

Variant summary

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

The XM_047419602.1(KIAA0319):​c.*931A>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 0.656 in 152,106 control chromosomes in the GnomAD database, including 33,320 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 0.66 (33320 hom., cov: 32)
• Consequence: KIAA0319 XM_047419602.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 5 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA0319	XM_047419602.1	c.*931A>G		3_prime_UTR_variant	Exon 21 of 21		XP_047275558.1
KIAA0319	XM_017011546.3	c.*931A>G		3_prime_UTR_variant	Exon 19 of 19		XP_016867035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99764 AN: 151988 Hom.: 33304 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.656 AC: 99810 AN: 152106 Hom.: 33320 Cov.: 32 AF XY: 0.653 AC XY: 48531 AN XY: 74352

African (AFR) AF: 0.685 AC: 28427 AN: 41484

American (AMR) AF: 0.538 AC: 8226 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2601 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1749 AN: 5182

South Asian (SAS) AF: 0.583 AC: 2813 AN: 4826

European-Finnish (FIN) AF: 0.688 AC: 7265 AN: 10566

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46749 AN: 67988

Other (OTH) AF: 0.646 AC: 1361 AN: 2106

Alfa AF: 0.678 Hom.: 58535

Bravo AF: 0.645

Asia WGS AF: 0.489 AC: 1703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.43
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2744604; hg19: chr6-24540539;