rs13313604

chr18-37042902-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.577-23988C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,058 control chromosomes in the GnomAD database, including 1,819 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 0.15 (1819 hom., cov: 32)
• Consequence: KIAA1328 NM_020776.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

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=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1328	NM_020776.3	c.577-23988C>T		intron_variant		ENST00000280020.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1328	ENST00000280020.10	c.577-23988C>T		intron_variant		1	NM_020776.3	P1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22796 AN: 151940 Hom.: 1813 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.150 AC: 22817 AN: 152058 Hom.: 1819 Cov.: 32 AF XY: 0.150 AC XY: 11186 AN XY: 74328

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.135

Alfa AF: 0.139 Hom.: 726

Bravo AF: 0.151

Asia WGS AF: 0.134 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	13
Dann	Benign	0.93

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: rs13313604; hg19: chr18-34622865;