18-37225231-C-T

Position:

• chr18-37225231-C-T

Variant summary

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

The ENST00000280020.10(KIAA1328):​c.*3004C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 985,326 control chromosomes in the GnomAD database, including 8,688 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 0.11 (1085 hom., cov: 32)
  • Exomes 𝑓: 0.13 (7603 hom.)
• Consequence: KIAA1328 ENST00000280020.10 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1328	NM_020776.3	c.*3004C>T		3_prime_UTR_variant	10/10	ENST00000280020.10	NP_065827.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1328	ENST00000280020.10	c.*3004C>T		3_prime_UTR_variant	10/10	1	NM_020776.3	ENSP00000280020	P1
KIAA1328	ENST00000591619.5	c.*3004C>T		3_prime_UTR_variant	10/11	1		ENSP00000465550
KIAA1328	ENST00000592611.5	c.*1283+3114C>T		intron_variant, NMD_transcript_variant		2		ENSP00000468653

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16214 AN: 152120 Hom.: 1084 Cov.: 32

Gnomad AFR AF: 0.0320

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.112

GnomAD4 exome AF: 0.134 AC: 111319 AN: 833088 Hom.: 7603 Cov.: 31 AF XY: 0.134 AC XY: 51694 AN XY: 384714

Gnomad4 AFR exome AF: 0.0207

Gnomad4 AMR exome AF: 0.111

Gnomad4 ASJ exome AF: 0.193

Gnomad4 EAS exome AF: 0.113

Gnomad4 SAS exome AF: 0.115

Gnomad4 FIN exome AF: 0.174

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.132

GnomAD4 genome AF: 0.106 AC: 16206 AN: 152238 Hom.: 1085 Cov.: 32 AF XY: 0.108 AC XY: 8074 AN XY: 74436

Gnomad4 AFR AF: 0.0319

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.111

Alfa AF: 0.123 Hom.: 476

Bravo AF: 0.101

Asia WGS AF: 0.131 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.56

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: rs2017027; hg19: chr18-34805194;