rs10502668

Positions:

• chr18-36922629-A-G

Variant summary

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

The NM_020776.3(KIAA1328):​c.449-36679A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,172 control chromosomes in the GnomAD database, including 1,073 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 0.10 (1073 hom., cov: 32)
• Consequence: KIAA1328 NM_020776.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538

Genes affected

KIAA1328 (HGNC:29248): (KIAA1328)

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1328	NM_020776.3	c.449-36679A>G		intron_variant		ENST00000280020.10
LOC105372069	NR_134585.1	n.41+1145T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1328	ENST00000280020.10	c.449-36679A>G		intron_variant		1	NM_020776.3	P1
	ENST00000586106.1	n.41+1145T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15831 AN: 152054 Hom.: 1072 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.104 AC: 15820 AN: 152172 Hom.: 1073 Cov.: 32 AF XY: 0.106 AC XY: 7878 AN XY: 74398

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.105

Alfa AF: 0.127 Hom.: 640

Bravo AF: 0.0973

Asia WGS AF: 0.122 AC: 425 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.42

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: rs10502668; hg19: chr18-34502592;