rs382518

Variant names:

• chr12-68386307-T-C
• rs382518
• ENST00000441255.7:n.308-2705A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441255.7(LINC02384):​n.308-2705A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,180 control chromosomes in the GnomAD database, including 1,193 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 (1193 hom., cov: 32)
• Consequence: LINC02384 ENST00000441255.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.02
• Publications: 3 publications found

Genes affected

LINC02384 (HGNC:53308): (long intergenic non-protein coding RNA 2384)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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
LINC02384	ENST00000441255.7	n.308-2705A>G		intron_variant	Intron 3 of 3	4
LINC02384	ENST00000539404.1	n.68+17426A>G		intron_variant	Intron 1 of 1	3
LINC02384	ENST00000546086.1	n.154-52643A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17461 AN: 152062 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0884

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

GnomAD4 genome AF: 0.115 AC: 17469 AN: 152180 Hom.: 1193 Cov.: 32 AF XY: 0.111 AC XY: 8250 AN XY: 74410

African (AFR) AF: 0.178 AC: 7398 AN: 41484

American (AMR) AF: 0.0590 AC: 902 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3468

East Asian (EAS) AF: 0.0241 AC: 125 AN: 5180

South Asian (SAS) AF: 0.0538 AC: 259 AN: 4812

European-Finnish (FIN) AF: 0.0831 AC: 881 AN: 10606

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7487 AN: 68016

Other (OTH) AF: 0.0870 AC: 184 AN: 2114

Alfa AF: 0.103 Hom.: 1187

Bravo AF: 0.113

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	16
DANN	Benign	0.93
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs382518; hg19: chr12-68780087;