rs9323783

Variant names:

• chr14-86145022-C-T
• rs9323783
• ENST00000655493.1:n.391-15842C>T

Variant summary

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

The ENST00000655493.1(LINC02328):​n.391-15842C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,888 control chromosomes in the GnomAD database, including 2,657 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 0.18 (2657 hom., cov: 32)
• Consequence: LINC02328 ENST00000655493.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

LINC02328 (HGNC:53248): (long intergenic non-protein coding RNA 2328)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02328	ENST00000655493.1	n.391-15842C>T		intron_variant	Intron 1 of 1
LINC02328	ENST00000668344.3	n.526-15842C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27161 AN: 151770 Hom.: 2648 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.179 AC: 27191 AN: 151888 Hom.: 2657 Cov.: 32 AF XY: 0.185 AC XY: 13717 AN XY: 74202

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.181

Alfa AF: 0.164 Hom.: 4183

Bravo AF: 0.183

Asia WGS AF: 0.213 AC: 739 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9323783; hg19: chr14-86611366;