rs10502669

Variant names:

• chr18-36924544-C-A
• rs10502669
• NM_020776.3:c.449-34764C>A

Your query was ambiguous. Multiple possible variants found:

• chr18-36924544-C-A
• chr18-36924544-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

KIAA1328 (HGNC:29248): (KIAA1328)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020776.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1328	NM_020776.3	MANE Select	c.449-34764C>A		intron	N/A	NP_065827.1
	KIAA1328	NM_001353918.2		c.449-34776C>A		intron	N/A	NP_001340847.1
	KIAA1328	NM_001322327.2		c.125-34764C>A		intron	N/A	NP_001309256.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1328	ENST00000280020.10	TSL:1 MANE Select	c.449-34764C>A		intron	N/A	ENSP00000280020.5
	KIAA1328	ENST00000591619.5	TSL:1	c.437-34764C>A		intron	N/A	ENSP00000465550.1
	KIAA1328	ENST00000586135.1	TSL:1	c.-676-368C>A		intron	N/A	ENSP00000467507.1

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

African (AFR) AF: 0.415 AC: 17158 AN: 41364

American (AMR) AF: 0.821 AC: 12551 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2785 AN: 3468

East Asian (EAS) AF: 0.874 AC: 4509 AN: 5158

South Asian (SAS) AF: 0.887 AC: 4259 AN: 4804

European-Finnish (FIN) AF: 0.842 AC: 8920 AN: 10590

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58727 AN: 67980

Other (OTH) AF: 0.786 AC: 1658 AN: 2110

Alfa AF: 0.812 Hom.: 19937

Bravo AF: 0.717

Asia WGS AF: 0.843 AC: 2927 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		0.028
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: rs10502669; hg19: chr18-34504507;