rs12098564

Positions:

• chr10-85193571-A-G
• chr10-85193571-A-T

Variant summary

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

The NR_120667.1(LINC01519):​n.1897T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0711 in 152,206 control chromosomes in the GnomAD database, including 967 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 0.071 (967 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01519 NR_120667.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332

Genes affected

LINC01519 (HGNC:51217): (long intergenic non-protein coding RNA 1519)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01519	NR_120667.1	n.1897T>C		non_coding_transcript_exon_variant	4/4
LINC01519	NR_120668.1	n.1050T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01519	ENST00000454178.1	n.1879T>C		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10803 AN: 152086 Hom.: 969 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0508

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.0128

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0266

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0150

Gnomad OTH AF: 0.0569

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0711 AC: 10825 AN: 152206 Hom.: 967 Cov.: 33 AF XY: 0.0701 AC XY: 5218 AN XY: 74422

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0509

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.0128

Gnomad4 SAS AF: 0.0180

Gnomad4 FIN AF: 0.0266

Gnomad4 NFE AF: 0.0151

Gnomad4 OTH AF: 0.0563

Alfa AF: 0.0276 Hom.: 212

Bravo AF: 0.0810

Asia WGS AF: 0.0360 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.86
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12098564; hg19: chr10-86953327;