rs736190

Positions:

• chr6-169380003-A-G

Variant summary

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

The ENST00000433388.6(LINC02519):​n.185+8198T>C 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 0.869 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 ENST00000433388.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02519	XR_007059890.1	n.206+8198T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02519	ENST00000433388.6	n.185+8198T>C		intron_variant, non_coding_transcript_variant		3
LINC02519	ENST00000440168.1	n.186-4226T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.831

Gnomad4 OTH AF: 0.866

Alfa AF: 0.853 Hom.: 6884

Bravo AF: 0.871

Asia WGS AF: 0.947 AC: 3293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs736190; hg19: chr6-169780098;