rs2817241

chr6-24542035-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.3041-690C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,116 control chromosomes in the GnomAD database, including 13,716 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 0.41 (13716 hom., cov: 33)
• Consequence: KIAA0319 XM_047419602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

Genes affected

KIAA0319 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0319	XM_017011546.3	c.2858-690C>T		intron_variant
KIAA0319	XM_017011550.2	c.*13-690C>T		intron_variant
KIAA0319	XM_047419602.1	c.3041-690C>T		intron_variant
KIAA0319	XM_047419604.1	c.*13-690C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61802 AN: 151996 Hom.: 13723 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.406 AC: 61788 AN: 152116 Hom.: 13716 Cov.: 33 AF XY: 0.407 AC XY: 30282 AN XY: 74358

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.404

Alfa AF: 0.456 Hom.: 2080

Bravo AF: 0.385

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.4
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2817241; hg19: chr6-24542263;