rs323311

chr18-37159141-C-Gchr18-37159141-C-T

Variant summary

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

The NM_020776.3(KIAA1328):c.1233-1059C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,572 control chromosomes in the GnomAD database, including 8,500 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 0.27 (8500 hom., cov: 32)
• Consequence: KIAA1328 NM_020776.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1328	NM_020776.3	c.1233-1059C>G		intron_variant		ENST00000280020.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1328	ENST00000280020.10	c.1233-1059C>G		intron_variant		1	NM_020776.3	P1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40489 AN: 151456 Hom.: 8482 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.268 AC: 40551 AN: 151572 Hom.: 8500 Cov.: 32 AF XY: 0.265 AC XY: 19591 AN XY: 74030

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.216

Alfa AF: 0.0720 Hom.: 110

Bravo AF: 0.283

Asia WGS AF: 0.160 AC: 558 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.0
Dann	Benign	0.77

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: rs323311; hg19: chr18-34739104;