rs10502669

chr18-36924544-C-Achr18-36924544-C-G

Variant summary

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

The NM_020776.3(KIAA1328):c.449-34764C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 151,962 control chromosomes in the GnomAD database, including 44,021 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 0.73 (44021 hom., cov: 31)
• Consequence: KIAA1328 NM_020776.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

Genes affected

KIAA1328 (HGNC:29248): (KIAA1328)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1328	NM_020776.3	c.449-34764C>A		intron_variant		ENST00000280020.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1328	ENST00000280020.10	c.449-34764C>A		intron_variant		1	NM_020776.3	P1

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111508 AN: 151844 Hom.: 44006 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.734 AC: 111565 AN: 151962 Hom.: 44021 Cov.: 31 AF XY: 0.737 AC XY: 54771 AN XY: 74284

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.786

Alfa AF: 0.809 Hom.: 12700

Bravo AF: 0.717

Asia WGS AF: 0.843 AC: 2927 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.9
Dann	Benign	0.43

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502669; hg19: chr18-34504507;