rs73009150

Positions:

• chr11-116497358-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_174967.1(LINC02151):​n.515G>A 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 0.0342 in 152,328 control chromosomes in the GnomAD database, including 119 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 0.034 (119 hom., cov: 33)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: LINC02151 NR_174967.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550

Genes affected

LINC02151 (HGNC:53013): (long intergenic non-protein coding RNA 2151)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0341 (5200/152280) while in subpopulation NFE AF= 0.0501 (3404/67966). AF 95% confidence interval is 0.0487. There are 119 homozygotes in gnomad4. There are 2499 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 119 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02151	NR_174967.1	n.515G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02151	ENST00000452629.2	n.482G>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.0342 AC: 5200 AN: 152162 Hom.: 119 Cov.: 33

Gnomad AFR AF: 0.00772

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0344

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00600

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0440

GnomAD4 exome AF: 0.104 AC: 5 AN: 48 Hom.: 0 Cov.: 0 AF XY: 0.0333 AC XY: 1 AN XY: 30

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.0833

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0341 AC: 5200 AN: 152280 Hom.: 119 Cov.: 33 AF XY: 0.0336 AC XY: 2499 AN XY: 74484

Gnomad4 AFR AF: 0.00769

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.0344

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00600

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.0501

Gnomad4 OTH AF: 0.0435

Alfa AF: 0.0437 Hom.: 39

Bravo AF: 0.0323

Asia WGS AF: 0.00404 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73009150; hg19: chr11-116368075;