ENST00000433388.7:n.207+7683A>G

Variant names:

• chr6-169380518-T-C
• rs9294997
• ENST00000433388.7:n.207+7683A>G

Variant summary

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

The ENST00000433388.7(LINC02519):​n.207+7683A>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 ENST00000433388.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.853
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433388.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02519	NR_187217.1		n.206+7683A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02519	ENST00000433388.7	TSL:3	n.207+7683A>G		intron	N/A
	LINC02519	ENST00000440168.1	TSL:2	n.186-4741A>G		intron	N/A
	LINC02519	ENST00000809422.1		n.176+7683A>G		intron	N/A

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

African (AFR) AF: 0.568 AC: 23539 AN: 41472

American (AMR) AF: 0.337 AC: 5155 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3470

East Asian (EAS) AF: 0.611 AC: 3158 AN: 5168

South Asian (SAS) AF: 0.260 AC: 1251 AN: 4816

European-Finnish (FIN) AF: 0.189 AC: 2000 AN: 10586

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9984 AN: 68010

Other (OTH) AF: 0.268 AC: 566 AN: 2112

Alfa AF: 0.234 Hom.: 2459

Bravo AF: 0.329

Asia WGS AF: 0.387 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.84
PhyloP100		0.85

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9294997;

hg19: chr6-169780613;