6-169380518-T-C

Variant names:

• chr6-169380518-T-C
• rs9294997
• ENST00000433388.6:n.185+7683A>G

Variant summary

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

The ENST00000440168.1(LINC02519):​n.186-4741A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,126 control chromosomes in the GnomAD database, including 9,942 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 0.31 (9942 hom., cov: 33)
• Consequence: LINC02519 ENST00000440168.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.853

Genes affected

LINC02519 (HGNC:53510): (long intergenic non-protein coding RNA 2519)

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 (EAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02519	NR_187217.1	n.206+7683A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02519	ENST00000433388.6	n.185+7683A>G		intron_variant	Intron 1 of 1	3
LINC02519	ENST00000440168.1	n.186-4741A>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46367 AN: 152010 Hom.: 9918 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.305 AC: 46447 AN: 152126 Hom.: 9942 Cov.: 33 AF XY: 0.308 AC XY: 22919 AN XY: 74390

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.268

Alfa AF: 0.235 Hom.: 2089

Bravo AF: 0.329

Asia WGS AF: 0.387 AC: 1343 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	4.9
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9294997; hg19: chr6-169780613;