rs9323783

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000668344.4	n.568-15842C>T		intron_variant	Intron 3 of 3
LINC02328	ENST00000752522.1	n.433-15842C>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

African (AFR) AF: 0.161 AC: 6675 AN: 41404

American (AMR) AF: 0.264 AC: 4026 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3468

East Asian (EAS) AF: 0.227 AC: 1166 AN: 5146

South Asian (SAS) AF: 0.243 AC: 1171 AN: 4812

European-Finnish (FIN) AF: 0.197 AC: 2069 AN: 10492

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.160 AC: 10898 AN: 67988

Other (OTH) AF: 0.181 AC: 382 AN: 2110

Alfa AF: 0.167 Hom.: 6567

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9323783; hg19: chr14-86611366;