NM_020776.3:c.576+37392A>G

Variant names:

• chr18-36996827-A-G
• rs880714
• NM_020776.3:c.576+37392A>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.576+37392A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,150 control chromosomes in the GnomAD database, including 28,885 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 0.60 (28885 hom., cov: 33)
• Consequence: KIAA1328 NM_020776.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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.576+37392A>G		intron	N/A	NP_065827.1	Q86T90-1
	KIAA1328	NM_001353918.2		c.564+37392A>G		intron	N/A	NP_001340847.1
	KIAA1328	NM_001322327.2		c.252+37392A>G		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.576+37392A>G		intron	N/A	ENSP00000280020.5	Q86T90-1
	KIAA1328	ENST00000591619.5	TSL:1	c.564+37392A>G		intron	N/A	ENSP00000465550.1	Q86T90-2
	KIAA1328	ENST00000586135.1	TSL:1	c.-277+50310A>G		intron	N/A	ENSP00000467507.1	Q86T90-3

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90636 AN: 152032 Hom.: 28884 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.596 AC: 90673 AN: 152150 Hom.: 28885 Cov.: 33 AF XY: 0.600 AC XY: 44590 AN XY: 74362

African (AFR) AF: 0.362 AC: 15037 AN: 41500

American (AMR) AF: 0.636 AC: 9726 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2087 AN: 3472

East Asian (EAS) AF: 0.872 AC: 4514 AN: 5174

South Asian (SAS) AF: 0.775 AC: 3741 AN: 4824

European-Finnish (FIN) AF: 0.672 AC: 7112 AN: 10578

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46276 AN: 68000

Other (OTH) AF: 0.632 AC: 1335 AN: 2112

Alfa AF: 0.502 Hom.: 1686

Bravo AF: 0.582

Asia WGS AF: 0.787 AC: 2733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.57
PhyloP100		-0.44
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: rs880714; hg19: chr18-34576790;