rs807526

Positions:

• chr6-24543492-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047419602.1(KIAA0319):​c.3041-2147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,850 control chromosomes in the GnomAD database, including 5,541 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 (5541 hom., cov: 32)
• Consequence: KIAA0319 XM_047419602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951

Genes affected

KIAA0319 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0319	XM_017011546.3	c.2858-2147C>T		intron_variant
KIAA0319	XM_017011550.2	c.*13-2147C>T		intron_variant
KIAA0319	XM_047419602.1	c.3041-2147C>T		intron_variant
KIAA0319	XM_047419604.1	c.*13-2147C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40071 AN: 151732 Hom.: 5521 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.264 AC: 40138 AN: 151850 Hom.: 5541 Cov.: 32 AF XY: 0.259 AC XY: 19187 AN XY: 74192

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.246

Alfa AF: 0.262 Hom.: 660

Bravo AF: 0.265

Asia WGS AF: 0.228 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs807526; hg19: chr6-24543720;