6-24579639-G-C

Variant names:

• chr6-24579639-G-C
• rs807507
• NM_014809.4:c.1372+219C>G

Variant summary

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

The NM_014809.4(KIAA0319):​c.1372+219C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 150,246 control chromosomes in the GnomAD database, including 33,196 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 0.65 (33196 hom., cov: 26)
• Consequence: KIAA0319 NM_014809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 8 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 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.1372+219C>G		intron	N/A	NP_055624.2	Q5VV43-1
	KIAA0319	NM_001168375.2		c.1372+219C>G		intron	N/A	NP_001161847.1	Q5VV43-1
	KIAA0319	NM_001350403.2		c.1372+219C>G		intron	N/A	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.1372+219C>G		intron	N/A	ENSP00000367459.3	Q5VV43-1
	KIAA0319	ENST00000537886.5	TSL:1	c.1372+219C>G		intron	N/A	ENSP00000439700.1	Q5VV43-4
	KIAA0319	ENST00000616673.4	TSL:1	c.-357+219C>G		intron	N/A	ENSP00000483665.1	A0A087X0U9

Frequencies

GnomAD3 genomes AF: 0.651 AC: 97725 AN: 150154 Hom.: 33136 Cov.: 26

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.651 AC: 97839 AN: 150246 Hom.: 33196 Cov.: 26 AF XY: 0.653 AC XY: 47843 AN XY: 73304

African (AFR) AF: 0.841 AC: 34264 AN: 40726

American (AMR) AF: 0.674 AC: 10108 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1667 AN: 3452

East Asian (EAS) AF: 0.804 AC: 4127 AN: 5136

South Asian (SAS) AF: 0.680 AC: 3246 AN: 4776

European-Finnish (FIN) AF: 0.570 AC: 5774 AN: 10136

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.540 AC: 36589 AN: 67766

Other (OTH) AF: 0.632 AC: 1304 AN: 2064

Alfa AF: 0.412 Hom.: 976

Bravo AF: 0.669

Asia WGS AF: 0.765 AC: 2660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.58
PhyloP100		-0.098
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: rs807507; hg19: chr6-24579867;