chr6-169380003-A-G

Variant names:

• chr6-169380003-A-G
• rs736190
• ENST00000433388.7:n.207+8198T>C

Variant summary

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

The ENST00000440168.1(LINC02519):​n.186-4226T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,308 control chromosomes in the GnomAD database, including 57,714 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 0.87 (57714 hom., cov: 34)
• Consequence: LINC02519 ENST00000440168.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440168.1. 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+8198T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02519	ENST00000433388.7	TSL:3	n.207+8198T>C		intron	N/A
	LINC02519	ENST00000440168.1	TSL:2	n.186-4226T>C		intron	N/A
	LINC02519	ENST00000809422.1		n.176+8198T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132299 AN: 152190 Hom.: 57663 Cov.: 34

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.869 AC: 132411 AN: 152308 Hom.: 57714 Cov.: 34 AF XY: 0.874 AC XY: 65085 AN XY: 74474

African (AFR) AF: 0.906 AC: 37656 AN: 41564

American (AMR) AF: 0.893 AC: 13668 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2949 AN: 3472

East Asian (EAS) AF: 0.964 AC: 4991 AN: 5178

South Asian (SAS) AF: 0.940 AC: 4542 AN: 4830

European-Finnish (FIN) AF: 0.866 AC: 9193 AN: 10616

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56563 AN: 68026

Other (OTH) AF: 0.866 AC: 1827 AN: 2110

Alfa AF: 0.855 Hom.: 7207

Bravo AF: 0.871

Asia WGS AF: 0.947 AC: 3293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.044
DANN	Benign	0.60
PhyloP100		-2.0

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: rs736190;

hg19: chr6-169780098;