rs9323783

Positions:

• chr14-86145022-C-T

Variant summary

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

The ENST00000668344.3(LINC02328):​n.526-15842C>T variant causes a intron, non coding transcript 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 ENST00000668344.3 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02328	ENST00000668344.3	n.526-15842C>T		intron_variant, non_coding_transcript_variant
LINC02328	ENST00000655493.1	n.391-15842C>T		intron_variant, non_coding_transcript_variant

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;