rs1445527

Variant names:

• chr18-36935916-T-A
• rs1445527
• NM_020776.3:c.449-23392T>A

Your query was ambiguous. Multiple possible variants found:

• chr18-36935916-T-A
• chr18-36935916-T-C
• chr18-36935916-T-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.449-23392T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,084 control chromosomes in the GnomAD database, including 43,990 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 (43990 hom., cov: 31)
• Consequence: KIAA1328 NM_020776.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404
• Publications: 1 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=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.863 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1328	NM_020776.3	MANE Select	c.449-23392T>A		intron	N/A	NP_065827.1	Q86T90-1
	KIAA1328	NM_001353918.2		c.449-23404T>A		intron	N/A	NP_001340847.1
	KIAA1328	NM_001322327.2		c.125-23392T>A		intron	N/A	NP_001309256.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1328	ENST00000280020.10	TSL:1 MANE Select	c.449-23392T>A		intron	N/A	ENSP00000280020.5	Q86T90-1
	KIAA1328	ENST00000591619.5	TSL:1	c.437-23392T>A		intron	N/A	ENSP00000465550.1	Q86T90-2
	KIAA1328	ENST00000586135.1	TSL:1	c.-545-10333T>A		intron	N/A	ENSP00000467507.1	Q86T90-3

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111467 AN: 151966 Hom.: 43975 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.733 AC: 111524 AN: 152084 Hom.: 43990 Cov.: 31 AF XY: 0.736 AC XY: 54760 AN XY: 74354

African (AFR) AF: 0.413 AC: 17108 AN: 41448

American (AMR) AF: 0.820 AC: 12526 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2786 AN: 3470

East Asian (EAS) AF: 0.875 AC: 4520 AN: 5168

South Asian (SAS) AF: 0.885 AC: 4273 AN: 4826

European-Finnish (FIN) AF: 0.843 AC: 8912 AN: 10576

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

European-Non Finnish (NFE) AF: 0.864 AC: 58747 AN: 68008

Other (OTH) AF: 0.785 AC: 1654 AN: 2108

Alfa AF: 0.784 Hom.: 6100

Bravo AF: 0.717

Asia WGS AF: 0.844 AC: 2931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	6.3
DANN	Benign	0.60
PhyloP100		0.40
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: rs1445527; hg19: chr18-34515879;