rs10520852

Positions:

• chr5-17892328-T-A
• chr5-17892328-T-C

Variant summary

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

The NR_134286.1(LINC02223):​n.578+19242T>A 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 0.0128 in 152,268 control chromosomes in the GnomAD database, including 21 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 0.013 (21 hom., cov: 32)
• Consequence: LINC02223 NR_134286.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

LINC02223 (HGNC:53092): (long intergenic non-protein coding RNA 2223)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0128 (1956/152268) while in subpopulation SAS AF= 0.0482 (232/4816). AF 95% confidence interval is 0.0431. There are 21 homozygotes in gnomad4. There are 955 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 21 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02223	NR_134286.1	n.578+19242T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02223	ENST00000511596.5	n.196-27899T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0128 AC: 1955 AN: 152150 Hom.: 21 Cov.: 32

Gnomad AFR AF: 0.00355

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.00557

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0477

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0128 AC: 1956 AN: 152268 Hom.: 21 Cov.: 32 AF XY: 0.0128 AC XY: 955 AN XY: 74470

Gnomad4 AFR AF: 0.00354

Gnomad4 AMR AF: 0.00556

Gnomad4 ASJ AF: 0.0231

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0482

Gnomad4 FIN AF: 0.0123

Gnomad4 NFE AF: 0.0181

Gnomad4 OTH AF: 0.0166

Alfa AF: 0.00346 Hom.: 2

Bravo AF: 0.0111

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.32
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520852; hg19: chr5-17892437;