18-36996827-A-G

Position:

• chr18-36996827-A-G

Variant summary

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

The ENST00000280020.10(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 ENST00000280020.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1328	NM_020776.3	c.576+37392A>G		intron_variant		ENST00000280020.10	NP_065827.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1328	ENST00000280020.10	c.576+37392A>G		intron_variant		1	NM_020776.3	ENSP00000280020	P1

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

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.632

Alfa AF: 0.514 Hom.: 1632

Bravo AF: 0.582

Asia WGS AF: 0.787 AC: 2733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.57

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: rs880714; hg19: chr18-34576790;